Dear Qixu,
You can take a look at existing entries which have link records between
1_555 and another symmetry molecule. For example 5BQC which has various
of these.
mmCIF:
#
loop_
_struct_conn.id
_struct_conn.conn_type_id
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_PDB_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.details
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
_struct_conn.pdbx_role
disulf1 disulf ? ? A CYS 7 SG ? ? ? 1_555 A CYS 68 SG ? ? B CYS 45 B
CYS 106 1_555 ? ? ? ? ? ? ? 2.032 ? ?
disulf2 disulf ? ? A CYS 15 SG ? ? ? 1_555 A CYS 61 SG ? ? B CYS 53 B
CYS 99 1_555 ? ? ? ? ? ? ? 2.031 ? ?
disulf3 disulf ? ? A CYS 52 SG ? ? ? 1_555 A CYS 90 SG ? ? B CYS 90 B
CYS 128 1_555 ? ? ? ? ? ? ? 2.027 ? ?
disulf4 disulf ? ? A CYS 79 SG ? ? ? 1_555 A CYS 120 SG ? ? B CYS 117 B
CYS 158 1_555 ? ? ? ? ? ? ? 2.030 ? ?
disulf5 disulf ? ? A CYS 83 SG ? ? ? 1_555 A CYS 107 SG ? ? B CYS 121 B
CYS 145 1_555 ? ? ? ? ? ? ? 2.031 ? ?
disulf6 disulf ? ? B CYS 18 SG ? ? ? 1_555 B CYS 75 SG ? ? A CYS 39 A
CYS 96 1_555 ? ? ? ? ? ? ? 2.009 ? ?
disulf7 disulf ? ? B CYS 34 SG ? ? ? 1_555 B CYS 89 SG ? ? A CYS 55 A
CYS 110 1_555 ? ? ? ? ? ? ? 2.029 ? ?
disulf8 disulf ? ? B CYS 44 SG ? ? ? 1_555 B CYS 105 SG ? ? A CYS 65 A
CYS 126 1_555 ? ? ? ? ? ? ? 2.039 ? ?
disulf9 disulf ? ? B CYS 48 SG ? ? ? 1_555 B CYS 107 SG ? ? A CYS 69 A
CYS 128 1_555 ? ? ? ? ? ? ? 2.010 ? ?
disulf10 disulf ? ? B CYS 72 SG ? ? ? 1_555 B CYS 74 SG ? ? A CYS 93 A
CYS 95 7_555 ? ? ? ? ? ? ? 1.996 ? ?
covale1 covale one ? A ASN 21 ND2 ? ? ? 1_555 E NAG . C1 ? ? B ASN 59 B
NAG 202 1_555 ? ? ? ? ? ? ? 1.446 ?
N-Glycosylation
covale2 covale one ? A ASN 106 ND2 ? ? ? 1_555 D NAG . C1 ? ? B ASN 144 B
NAG 201 1_555 ? ? ? ? ? ? ? 1.440 ?
N-Glycosylation
covale3 covale none ? A HIS 116 NE2 ? ? ? 1_555 C GU4 . O29 ? ? B HIS 154 C
GU4 1 10_444 ? ? ? ? ? ? ? 1.458 ? ?
covale4 covale none ? B ARG 86 NH1 ? ? ? 1_555 C YYJ . C6 ? ? A ARG 107 C
YYJ 2 10_444 ? ? ? ? ? ? ? 1.287 ? ?
covale5 covale both ? C GU4 . C1 ? ? ? 1_555 C YYJ . O2 ? ? C GU4 1 C
YYJ 2 1_555 ? ? ? ? ? ? ? 1.370 sing ?
#
PDB:
LINK ND2 ASN B 59 C1 NAG B 202 1555 1555 1.45
LINK ND2 ASN B 144 C1 NAG B 201 1555 1555 1.44
LINK NE2 HIS B 154 O29 GU4 C 1 1555 10444 1.46
LINK NH1 ARG A 107 C6 YYJ C 2 1555 10444 1.29
LINK C1 GU4 C 1 O2 YYJ C 2 1555 1555 1.37
Let me know if you need further assistance.
Kind regards,
Deborah Harrus
PDBe
On 29/12/2023 12:12, Qixu Cai wrote:
Dear all,
I'm working on the refinement of a crystal structure. In the
structure, one crystal packing interface is mediated by a compound
with two coordinate covalent bonds to two macromolecules from
different asymmetric units. Thus I need to specify two "LINK" records
in the head of pdb file. The "LINK" record between the compound and
macromolecule in the same asymmetric unit is generated by refmac
automatically. However, refmac does not generate the other "LINK"
between the compound and the symmetric macromolecule.
Thus I want to add the LINK record myself. As the LINK is between
different symmetric molecules, I need to specify the symmetry code,
such as "1555", "2555" and so on. The symmetry code is dependent on
the "REMARK 290" record.
My question is:
1. How can I generate the "REMARK 290" information?
2. Any easier method to generate the "LINK" record between molecules
from different asymmetric units?
Thanks a lot for your help!
Best regards,
Qixu Cai
Email: caiq...@gmail.com
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-------------------------------------------------------------------
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
http://www.PDBe.org
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