PDB-2vml: The monoclinic structure of phycocyanin from Gloeobacter violaceus

ID or keywords:

Entry

Database: PDB / ID: 2vml

Title

The monoclinic structure of phycocyanin from Gloeobacter violaceus

Components

PHYCOCYANIN ALPHA CHAIN
PHYCOCYANIN BETA CHAIN

Keywords

PHOTOSYNTHESIS / LIGHT-HARVESTING / ELECTRON TRANSPORT / TRANSPORT / CHROMOPHORE / BILE PIGMENT / PHYCOBILISOME

Function / homology

Function and homology information

phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function

Biological species

GLOEOBACTER VIOLACEUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Murray, J.W. / Benson, S. / Barber, J.

Citation

Journal: To be Published
Title: The Structures of the Phycobiliproteins of Gloeobacter Violaceus
Authors: Murray, J.W. / Benson, S. / Nield, J. / Barber, J.

History

Deposition	Jan 28, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 25, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	May 8, 2019	Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2vml.cif.gz	406.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2vml.ent.gz	339.6 KB	Display	PDB format
PDBx/mmJSON format	2vml.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vm/2vml ftp://data.pdbj.org/pub/pdb/validation_reports/vm/2vml	HTTPS FTP

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Related structure data

Related structure data	2vjhC 2vjrSC 2vjtC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2vjr-1 1gh0-1 1phn-2 2uum-2 5o7m-1 2uul-2 2uum-1 1jbo-1 5mjq-1 4h0m-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: PHYCOCYANIN ALPHA CHAIN

B: PHYCOCYANIN BETA CHAIN

C: PHYCOCYANIN ALPHA CHAIN

D: PHYCOCYANIN BETA CHAIN

E: PHYCOCYANIN ALPHA CHAIN

F: PHYCOCYANIN BETA CHAIN

G: PHYCOCYANIN ALPHA CHAIN

H: PHYCOCYANIN BETA CHAIN

I: PHYCOCYANIN ALPHA CHAIN

J: PHYCOCYANIN BETA CHAIN

K: PHYCOCYANIN ALPHA CHAIN

L: PHYCOCYANIN BETA CHAIN

hetero molecules

228 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	86.877, 142.040, 115.313
Angle α, β, γ (deg.)	90.00, 107.65, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	C
3	1	E
4	1	G
5	1	I
6	1	K
1	2	B
2	2	D
3	2	F
4	2	H
5	2	J
6	2	L

NCS domain segments:

Refine code: 1

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	THR	THR	A	A	1 - 6	1 - 6
2	1	1	MET	MET	THR	THR	C	C	1 - 6	1 - 6
3	1	1	MET	MET	THR	THR	E	E	1 - 6	1 - 6
4	1	1	MET	MET	THR	THR	G	G	1 - 6	1 - 6
5	1	1	MET	MET	THR	THR	I	I	1 - 6	1 - 6
6	1	1	MET	MET	THR	THR	K	K	1 - 6	1 - 6
1	2	1	VAL	VAL	ALA	ALA	A	A	8 - 41	8 - 41
2	2	1	VAL	VAL	ALA	ALA	C	C	8 - 41	8 - 41
3	2	1	VAL	VAL	ALA	ALA	E	E	8 - 41	8 - 41
4	2	1	VAL	VAL	ALA	ALA	G	G	8 - 41	8 - 41
5	2	1	VAL	VAL	ALA	ALA	I	I	8 - 41	8 - 41
6	2	1	VAL	VAL	ALA	ALA	K	K	8 - 41	8 - 41
1	3	1	ALA	ALA	SER	SER	A	A	43 - 46	43 - 46
2	3	1	ALA	ALA	SER	SER	C	C	43 - 46	43 - 46
3	3	1	ALA	ALA	SER	SER	E	E	43 - 46	43 - 46
4	3	1	ALA	ALA	SER	SER	G	G	43 - 46	43 - 46
5	3	1	ALA	ALA	SER	SER	I	I	43 - 46	43 - 46
6	3	1	ALA	ALA	SER	SER	K	K	43 - 46	43 - 46
1	4	1	ALA	ALA	VAL	VAL	A	A	48 - 52	48 - 52
2	4	1	ALA	ALA	VAL	VAL	C	C	48 - 52	48 - 52
3	4	1	ALA	ALA	VAL	VAL	E	E	48 - 52	48 - 52
4	4	1	ALA	ALA	VAL	VAL	G	G	48 - 52	48 - 52
5	4	1	ALA	ALA	VAL	VAL	I	I	48 - 52	48 - 52
6	4	1	ALA	ALA	VAL	VAL	K	K	48 - 52	48 - 52
1	5	1	GLY	GLY	VAL	VAL	A	A	54 - 56	54 - 56
2	5	1	GLY	GLY	VAL	VAL	C	C	54 - 56	54 - 56
3	5	1	GLY	GLY	VAL	VAL	E	E	54 - 56	54 - 56
4	5	1	GLY	GLY	VAL	VAL	G	G	54 - 56	54 - 56
5	5	1	GLY	GLY	VAL	VAL	I	I	54 - 56	54 - 56
6	5	1	GLY	GLY	VAL	VAL	K	K	54 - 56	54 - 56
1	6	1	GLU	GLU	TYR	TYR	A	A	58 - 60	58 - 60
2	6	1	GLU	GLU	TYR	TYR	C	C	58 - 60	58 - 60
3	6	1	GLU	GLU	TYR	TYR	E	E	58 - 60	58 - 60
4	6	1	GLU	GLU	TYR	TYR	G	G	58 - 60	58 - 60
5	6	1	GLU	GLU	TYR	TYR	I	I	58 - 60	58 - 60
6	6	1	GLU	GLU	TYR	TYR	K	K	58 - 60	58 - 60
1	7	1	LYS	LYS	GLY	GLY	A	A	62 - 75	62 - 75
2	7	1	LYS	LYS	GLY	GLY	C	C	62 - 75	62 - 75
3	7	1	LYS	LYS	GLY	GLY	E	E	62 - 75	62 - 75
4	7	1	LYS	LYS	GLY	GLY	G	G	62 - 75	62 - 75
5	7	1	LYS	LYS	GLY	GLY	I	I	62 - 75	62 - 75
6	7	1	LYS	LYS	GLY	GLY	K	K	62 - 75	62 - 75
1	8	1	THR	THR	ILE	ILE	A	A	77 - 86	77 - 86
2	8	1	THR	THR	ILE	ILE	C	C	77 - 86	77 - 86
3	8	1	THR	THR	ILE	ILE	E	E	77 - 86	77 - 86
4	8	1	THR	THR	ILE	ILE	G	G	77 - 86	77 - 86
5	8	1	THR	THR	ILE	ILE	I	I	77 - 86	77 - 86
6	8	1	THR	THR	ILE	ILE	K	K	77 - 86	77 - 86
1	9	1	TYR	TYR	ARG	ARG	A	A	89 - 114	89 - 114
2	9	1	TYR	TYR	ARG	ARG	C	C	89 - 114	89 - 114
3	9	1	TYR	TYR	ARG	ARG	E	E	89 - 114	89 - 114
4	9	1	TYR	TYR	ARG	ARG	G	G	89 - 114	89 - 114
5	9	1	TYR	TYR	ARG	ARG	I	I	89 - 114	89 - 114
6	9	1	TYR	TYR	ARG	ARG	K	K	89 - 114	89 - 114
1	10	1	VAL	VAL	PRO	PRO	A	A	116 - 124	116 - 124
2	10	1	VAL	VAL	PRO	PRO	C	C	116 - 124	116 - 124
3	10	1	VAL	VAL	PRO	PRO	E	E	116 - 124	116 - 124
4	10	1	VAL	VAL	PRO	PRO	G	G	116 - 124	116 - 124
5	10	1	VAL	VAL	PRO	PRO	I	I	116 - 124	116 - 124
6	10	1	VAL	VAL	PRO	PRO	K	K	116 - 124	116 - 124
1	11	1	TRP	TRP	LYS	LYS	A	A	126 - 132	126 - 132
2	11	1	TRP	TRP	LYS	LYS	C	C	126 - 132	126 - 132
3	11	1	TRP	TRP	LYS	LYS	E	E	126 - 132	126 - 132
4	11	1	TRP	TRP	LYS	LYS	G	G	126 - 132	126 - 132
5	11	1	TRP	TRP	LYS	LYS	I	I	126 - 132	126 - 132
6	11	1	TRP	TRP	LYS	LYS	K	K	126 - 132	126 - 132
1	12	1	ILE	ILE	SER	SER	A	A	134 - 140	134 - 140
2	12	1	ILE	ILE	SER	SER	C	C	134 - 140	134 - 140
3	12	1	ILE	ILE	SER	SER	E	E	134 - 140	134 - 140
4	12	1	ILE	ILE	SER	SER	G	G	134 - 140	134 - 140
5	12	1	ILE	ILE	SER	SER	I	I	134 - 140	134 - 140
6	12	1	ILE	ILE	SER	SER	K	K	134 - 140	134 - 140
1	13	1	LEU	LEU	SER	SER	A	A	142 - 162	142 - 162
2	13	1	LEU	LEU	SER	SER	C	C	142 - 162	142 - 162
3	13	1	LEU	LEU	SER	SER	E	E	142 - 162	142 - 162
4	13	1	LEU	LEU	SER	SER	G	G	142 - 162	142 - 162
5	13	1	LEU	LEU	SER	SER	I	I	142 - 162	142 - 162
6	13	1	LEU	LEU	SER	SER	K	K	142 - 162	142 - 162
1	14	1	CYC	CYC	CYC	CYC	A	M	1082
2	14	1	CYC	CYC	CYC	CYC	C	P	1082
3	14	1	CYC	CYC	CYC	CYC	E	S	1082
4	14	1	CYC	CYC	CYC	CYC	G	V	1082
5	14	1	CYC	CYC	CYC	CYC	I	Y	1082
6	14	1	CYC	CYC	CYC	CYC	K	BA	1082
1	1	2	MET	MET	SER	SER	B	B	1 - 20	1 - 20
2	1	2	MET	MET	SER	SER	D	D	1 - 20	1 - 20
3	1	2	MET	MET	SER	SER	F	F	1 - 20	1 - 20
4	1	2	MET	MET	SER	SER	H	H	1 - 20	1 - 20
5	1	2	MET	MET	SER	SER	J	J	1 - 20	1 - 20
6	1	2	MET	MET	SER	SER	L	L	1 - 20	1 - 20
1	2	2	GLN	GLN	LEU	LEU	B	B	22 - 24	22 - 24
2	2	2	GLN	GLN	LEU	LEU	D	D	22 - 24	22 - 24
3	2	2	GLN	GLN	LEU	LEU	F	F	22 - 24	22 - 24
4	2	2	GLN	GLN	LEU	LEU	H	H	22 - 24	22 - 24
5	2	2	GLN	GLN	LEU	LEU	J	J	22 - 24	22 - 24
6	2	2	GLN	GLN	LEU	LEU	L	L	22 - 24	22 - 24
1	3	2	LEU	LEU	THR	THR	B	B	27 - 28	27 - 28
2	3	2	LEU	LEU	THR	THR	D	D	27 - 28	27 - 28
3	3	2	LEU	LEU	THR	THR	F	F	27 - 28	27 - 28
4	3	2	LEU	LEU	THR	THR	H	H	27 - 28	27 - 28
5	3	2	LEU	LEU	THR	THR	J	J	27 - 28	27 - 28
6	3	2	LEU	LEU	THR	THR	L	L	27 - 28	27 - 28
1	4	2	LEU	LEU	ALA	ALA	B	B	30 - 49	30 - 49
2	4	2	LEU	LEU	ALA	ALA	D	D	30 - 49	30 - 49
3	4	2	LEU	LEU	ALA	ALA	F	F	30 - 49	30 - 49
4	4	2	LEU	LEU	ALA	ALA	H	H	30 - 49	30 - 49
5	4	2	LEU	LEU	ALA	ALA	J	J	30 - 49	30 - 49
6	4	2	LEU	LEU	ALA	ALA	L	L	30 - 49	30 - 49
1	5	2	ALA	ALA	ALA	ALA	B	B	55 - 56	55 - 56
2	5	2	ALA	ALA	ALA	ALA	D	D	55 - 56	55 - 56
3	5	2	ALA	ALA	ALA	ALA	F	F	55 - 56	55 - 56
4	5	2	ALA	ALA	ALA	ALA	H	H	55 - 56	55 - 56
5	5	2	ALA	ALA	ALA	ALA	J	J	55 - 56	55 - 56
6	5	2	ALA	ALA	ALA	ALA	L	L	55 - 56	55 - 56
1	6	2	LYS	LYS	PHE	PHE	B	B	58 - 60	58 - 60
2	6	2	LYS	LYS	PHE	PHE	D	D	58 - 60	58 - 60
3	6	2	LYS	LYS	PHE	PHE	F	F	58 - 60	58 - 60
4	6	2	LYS	LYS	PHE	PHE	H	H	58 - 60	58 - 60
5	6	2	LYS	LYS	PHE	PHE	J	J	58 - 60	58 - 60
6	6	2	LYS	LYS	PHE	PHE	L	L	58 - 60	58 - 60
1	7	2	GLN	GLN	THR	THR	B	B	63 - 64	63 - 64
2	7	2	GLN	GLN	THR	THR	D	D	63 - 64	63 - 64
3	7	2	GLN	GLN	THR	THR	F	F	63 - 64	63 - 64
4	7	2	GLN	GLN	THR	THR	H	H	63 - 64	63 - 64
5	7	2	GLN	GLN	THR	THR	J	J	63 - 64	63 - 64
6	7	2	GLN	GLN	THR	THR	L	L	63 - 64	63 - 64
1	8	2	LEU	LEU	MET	MET	B	B	66 - 86	66 - 86
2	8	2	LEU	LEU	MET	MET	D	D	66 - 86	66 - 86
3	8	2	LEU	LEU	MET	MET	F	F	66 - 86	66 - 86
4	8	2	LEU	LEU	MET	MET	H	H	66 - 86	66 - 86
5	8	2	LEU	LEU	MET	MET	J	J	66 - 86	66 - 86
6	8	2	LEU	LEU	MET	MET	L	L	66 - 86	66 - 86
1	9	2	ILE	ILE	LEU	LEU	B	B	88 - 105	88 - 105
2	9	2	ILE	ILE	LEU	LEU	D	D	88 - 105	88 - 105
3	9	2	ILE	ILE	LEU	LEU	F	F	88 - 105	88 - 105
4	9	2	ILE	ILE	LEU	LEU	H	H	88 - 105	88 - 105
5	9	2	ILE	ILE	LEU	LEU	J	J	88 - 105	88 - 105
6	9	2	ILE	ILE	LEU	LEU	L	L	88 - 105	88 - 105
1	10	2	ASP	ASP	THR	THR	B	B	107 - 124	107 - 124
2	10	2	ASP	ASP	THR	THR	D	D	107 - 124	107 - 124
3	10	2	ASP	ASP	THR	THR	F	F	107 - 124	107 - 124
4	10	2	ASP	ASP	THR	THR	H	H	107 - 124	107 - 124
5	10	2	ASP	ASP	THR	THR	J	J	107 - 124	107 - 124
6	10	2	ASP	ASP	THR	THR	L	L	107 - 124	107 - 124
1	11	2	SER	SER	VAL	VAL	B	B	126 - 131	126 - 131
2	11	2	SER	SER	VAL	VAL	D	D	126 - 131	126 - 131
3	11	2	SER	SER	VAL	VAL	F	F	126 - 131	126 - 131
4	11	2	SER	SER	VAL	VAL	H	H	126 - 131	126 - 131
5	11	2	SER	SER	VAL	VAL	J	J	126 - 131	126 - 131
6	11	2	SER	SER	VAL	VAL	L	L	126 - 131	126 - 131
1	12	2	MET	MET	ASN	ASN	B	B	134 - 143	134 - 143
2	12	2	MET	MET	ASN	ASN	D	D	134 - 143	134 - 143
3	12	2	MET	MET	ASN	ASN	F	F	134 - 143	134 - 143
4	12	2	MET	MET	ASN	ASN	H	H	134 - 143	134 - 143
5	12	2	MET	MET	ASN	ASN	J	J	134 - 143	134 - 143
6	12	2	MET	MET	ASN	ASN	L	L	134 - 143	134 - 143
1	13	2	GLY	GLY	THR	THR	B	B	147 - 149	147 - 149
2	13	2	GLY	GLY	THR	THR	D	D	147 - 149	147 - 149
3	13	2	GLY	GLY	THR	THR	F	F	147 - 149	147 - 149
4	13	2	GLY	GLY	THR	THR	H	H	147 - 149	147 - 149
5	13	2	GLY	GLY	THR	THR	J	J	147 - 149	147 - 149
6	13	2	GLY	GLY	THR	THR	L	L	147 - 149	147 - 149
1	14	2	GLY	GLY	VAL	VAL	B	B	151 - 157	151 - 157
2	14	2	GLY	GLY	VAL	VAL	D	D	151 - 157	151 - 157
3	14	2	GLY	GLY	VAL	VAL	F	F	151 - 157	151 - 157
4	14	2	GLY	GLY	VAL	VAL	H	H	151 - 157	151 - 157
5	14	2	GLY	GLY	VAL	VAL	J	J	151 - 157	151 - 157
6	14	2	GLY	GLY	VAL	VAL	L	L	151 - 157	151 - 157
1	15	2	GLU	GLU	ASP	ASP	B	B	159 - 165	159 - 165
2	15	2	GLU	GLU	ASP	ASP	D	D	159 - 165	159 - 165
3	15	2	GLU	GLU	ASP	ASP	F	F	159 - 165	159 - 165
4	15	2	GLU	GLU	ASP	ASP	H	H	159 - 165	159 - 165
5	15	2	GLU	GLU	ASP	ASP	J	J	159 - 165	159 - 165
6	15	2	GLU	GLU	ASP	ASP	L	L	159 - 165	159 - 165
1	16	2	ALA	ALA	ALA	ALA	B	B	167 - 172	167 - 172
2	16	2	ALA	ALA	ALA	ALA	D	D	167 - 172	167 - 172
3	16	2	ALA	ALA	ALA	ALA	F	F	167 - 172	167 - 172
4	16	2	ALA	ALA	ALA	ALA	H	H	167 - 172	167 - 172
5	16	2	ALA	ALA	ALA	ALA	J	J	167 - 172	167 - 172
6	16	2	ALA	ALA	ALA	ALA	L	L	167 - 172	167 - 172
1	17	2	CYC	CYC	CYC	CYC	B	N	1082
2	17	2	CYC	CYC	CYC	CYC	D	Q	1082
3	17	2	CYC	CYC	CYC	CYC	F	T	1082
4	17	2	CYC	CYC	CYC	CYC	H	W	1082
5	17	2	CYC	CYC	CYC	CYC	J	Z	1082
6	17	2	CYC	CYC	CYC	CYC	L	CA	1082

NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.28789, -0.76374, -0.57778), (-0.74193, 0.20361, -0.63882), (0.60553, 0.61258, -0.50802)	40.62193, 43.5993, 30.74681
2	given	(0.30531, -0.73857, 0.60108), (-0.75364, 0.19844, 0.62662), (-0.58208, -0.64431, -0.49603)	1.16895, 2.2471, 66.88448
3	given	(-0.31656, 0.71867, -0.61912), (0.71972, -0.24318, -0.65028), (-0.61789, -0.65145, -0.44026)	99.083, -37.11579, 66.85672
4	given	(-0.27692, 0.78019, 0.5609), (0.77886, -0.15962, 0.60655), (0.56275, 0.60483, -0.56346)	59.16881, -80.41515, 34.34856
5	given	(-0.99952, -0.00675, 0.03033), (0.00859, -0.9981, 0.061), (0.02986, 0.06123, 0.99768)	98.58434, -38.96901, -0.2577
6	given	(0.29065, -0.76066, -0.58045), (-0.74107, 0.20479, -0.63944), (0.60526, 0.61601, -0.50418)	40.57185, 43.46851, 30.76927
7	given	(0.30561, -0.73742, 0.60235), (-0.75054, 0.20272, 0.62897), (-0.58592, -0.6443, -0.49151)	1.21627, 2.17594, 67.05257
8	given	(-0.31102, 0.72077, -0.61948), (0.71753, -0.24935, -0.65036), (-0.62323, -0.64677, -0.43962)	98.84341, -37.17488, 67.1999
9	given	(-0.28296, 0.78063, 0.55727), (0.77312, -0.15823, 0.61421), (0.56764, 0.60464, -0.55874)	59.38138, -80.06272, 34.1606
10	given	(-0.99958, -0.00092, 0.0291), (0.00245, -0.9986, 0.05286), (0.02901, 0.0529, 0.99818)	98.70829, -38.72058, -0.29086

#1: Protein	PHYCOCYANIN ALPHA CHAIN Mass: 17679.852 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: PASTEUR CULTURE COLLECTION / Source: (natural) GLOEOBACTER VIOLACEUS (bacteria) / Strain: PCC7421 / References: UniProt: Q7M7F7
#2: Protein	PHYCOCYANIN BETA CHAIN Mass: 18478.953 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: PASTEUR CULTURE COLLECTION / Source: (natural) GLOEOBACTER VIOLACEUS (bacteria) / Strain: PCC7421 / References: UniProt: Q7M7C7
#3: Chemical	ChemComp-CYC / PHYCOCYANOBILIN Mass: 588.694 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C₃₃H₄₀N₄O₆
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 710 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3 Å³/Da / Density % sol: 58.97 % / Description: NONE
Crystal grow	Method: vapor diffusion, hanging drop Details: 8% PEG 4000, 0.1 M NA ACETATE PH 4.6 MIXED WITH IN EQUAL VOLUME OF 10MG/ML PROTEIN SOLUTION, HANGING DROP VAPOUR DIFFUSION

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.283
Detector	Type: MARRESEARCH / Detector: CCD / Date: Nov 8, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.283 Å / Relative weight: 1
Reflection	Resolution: 2.4→43.44 Å / Num. obs: 102846 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3.63 % / B_iso Wilson estimate: 44.82 Å² / R_merge(I) obs: 0.11 / Net I/σ(I): 8.94
Reflection shell	Resolution: 2.4→2.42 Å / Redundancy: 3.08 % / R_merge(I) obs: 0.33 / Mean I/σ(I) obs: 1.71 / % possible all: 93.7

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VJR

2vjr

Resolution: 2.4→109.76 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.926 / SU B: 13.245 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.347 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.218	5148	5.07 %	RANDOM
R_work	0.192	-	-	-
obs	0.194	102819	98.8 %	-

Solvent computation

Ion probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 28.18 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.371 Å²	0 Å²	-1.261 Å²
2-	-	-0.716 Å²	0 Å²
3-	-	-	-0.421 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→109.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15216	0	774	710	16700

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	16278
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.056	2.019	22116
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.417	5	1992
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.413	24.261	690
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.709	15	2580
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.683	15	114
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	2448
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	18396
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	3610
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	7720
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.175	0.2	702
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.198	0.2	17
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.209	0.2	13
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.813	1.5	12876
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.87	2	15840
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.699	3	7837
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.605	4.5	6276
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1953	tight positional	0.03	0.05
1	2	C	1953	tight positional	0.04	0.05
1	3	E	1953	tight positional	0.03	0.05
1	4	G	1953	tight positional	0.04	0.05
1	5	I	1953	tight positional	0.04	0.05
1	6	K	1953	tight positional	0.03	0.05
2	1	B	1884	tight positional	0.04	0.05
2	2	D	1884	tight positional	0.04	0.05
2	3	F	1884	tight positional	0.04	0.05
2	4	H	1884	tight positional	0.04	0.05
2	5	J	1884	tight positional	0.06	0.05
2	6	L	1884	tight positional	0.05	0.05
1	1	A	1953	tight thermal	0.09	0.5
1	2	C	1953	tight thermal	0.1	0.5
1	3	E	1953	tight thermal	0.09	0.5
1	4	G	1953	tight thermal	0.09	0.5
1	5	I	1953	tight thermal	0.1	0.5
1	6	K	1953	tight thermal	0.09	0.5
2	1	B	1884	tight thermal	0.09	0.5
2	2	D	1884	tight thermal	0.1	0.5
2	3	F	1884	tight thermal	0.08	0.5
2	4	H	1884	tight thermal	0.09	0.5
2	5	J	1884	tight thermal	0.11	0.5
2	6	L	1884	tight thermal	0.08	0.5

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.305	340	-
R_work	0.265	7667	-
obs	-	-	89.357 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.9319	1.148	-0.3417	1.348	-0.1847	0.6805	-0.0989	0.1113	0.0301	-0.213	0.0732	0.0453	0.0273	-0.0296	0.0257	-0.0618	0.025	-0.0364	-0.0416	-0.0203	-0.0872	30.19	-29.899	1.914
2	0.6285	0.448	0.4578	0.9811	0.1735	0.3687	-0.0782	-0.1546	0.1546	-0.0662	-0.0348	0.2492	-0.0375	-0.1676	0.113	-0.0348	0.0067	-0.0343	0.0471	-0.0279	0.0043	44.559	1.577	5.566
3	0.58	0.1551	-0.2379	0.9539	-0.4491	1.856	-0.0001	0.046	0.0218	-0.0733	-0.0074	0.0001	-0.0477	0.0408	0.0075	-0.1584	0.0268	-0.0035	-0.1212	-0.0234	-0.0764	71.025	13.899	29.733
4	1.5594	1.2822	-1.1148	1.3423	-0.8616	0.8074	0.017	0.0663	0.1109	0.0819	0.0648	0.2285	-0.0498	-0.1955	-0.0818	-0.0705	0.059	0.0339	-0.0203	-0.026	0.0274	49.105	7.224	55.911
5	1.1438	0.1675	0.3666	1.6061	0.7125	1.6224	0.0287	-0.2369	0.0595	0.2078	0.0175	0.0528	-0.0603	0.0016	-0.0462	-0.1239	0.0278	0.0678	0.0056	-0.0424	-0.0568	33.627	-25.226	67.623
6	0.7683	0.1113	0.3433	0.1349	-0.3912	2.323	0.001	-0.0851	0.0426	-0.0604	-0.0336	0.1423	-0.1393	-0.1969	0.0325	-0.128	0.0798	0.0025	-0.028	-0.0722	0.0544	17.01	-27.441	37.175
7	0.8571	0.4025	-0.4013	1.3356	-0.8939	2.1421	0.0731	-0.1935	0.0091	0.2741	-0.0344	-0.0208	-0.0842	-0.0425	-0.0387	-0.0784	0.0121	-0.0192	-0.06	-0.0024	-0.0563	66.855	-9.375	66.834
8	0.6636	0.1021	-0.1796	0.244	0.4457	1.6733	0.0549	0.0037	-0.1253	-0.0203	-0.0191	-0.0819	0.1257	0.0971	-0.0358	-0.1086	0.0596	-0.0017	-0.1015	0.0106	0.0388	82.7	-9.232	35.971
9	0.6343	0.2435	0.4957	0.8607	0.6098	2.0775	-0.0089	-0.0044	-0.0068	-0.1001	-0.0218	0.0616	0.0515	-0.0577	0.0307	-0.148	0.0265	0.0229	-0.1028	-0.0002	-0.0748	28.545	-50.965	32.153
10	1.3001	0.4999	0.598	0.9365	0.1645	0.6455	-0.0217	0.029	0.0381	-0.0158	-0.0156	-0.0409	-0.0545	0.0083	0.0373	-0.1094	0.0255	0.0073	-0.0961	0.0089	-0.0802	51.136	-42.448	57.28
11	1.7846	0.6909	0.2312	1.3892	0.0835	0.8888	-0.0834	0.1085	0.0433	-0.1791	0.1131	-0.0952	0.0013	0.0807	-0.0297	-0.0664	0.0229	0.039	-0.0544	-0.0407	-0.0857	68.702	-8.747	0.738
12	0.6819	0.6903	-0.6727	1.0944	-0.5947	0.6823	-0.0805	-0.1264	-0.1621	-0.1158	-0.011	-0.1333	0.0952	0.1236	0.0915	-0.0201	0.021	0.0382	0.0338	-0.0101	0.0381	54.3172	-40.0321	6.7944

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 162
2	X-RAY DIFFRACTION	1	A	1082
3	X-RAY DIFFRACTION	2	B	1 - 172
4	X-RAY DIFFRACTION	2	B	1082 - 1153
5	X-RAY DIFFRACTION	3	C	1 - 162
6	X-RAY DIFFRACTION	3	C	1082
7	X-RAY DIFFRACTION	4	D	1 - 172
8	X-RAY DIFFRACTION	4	D	1082 - 1153
9	X-RAY DIFFRACTION	5	E	1 - 162
10	X-RAY DIFFRACTION	5	E	1082
11	X-RAY DIFFRACTION	6	F	1 - 172
12	X-RAY DIFFRACTION	6	F	1082 - 1153
13	X-RAY DIFFRACTION	7	G	1 - 162
14	X-RAY DIFFRACTION	7	G	1082
15	X-RAY DIFFRACTION	8	H	1 - 172
16	X-RAY DIFFRACTION	8	H	1082 - 1153
17	X-RAY DIFFRACTION	9	I	1 - 162
18	X-RAY DIFFRACTION	9	I	1082
19	X-RAY DIFFRACTION	10	J	1 - 172
20	X-RAY DIFFRACTION	10	J	1082 - 1153
21	X-RAY DIFFRACTION	11	K	1 - 162
22	X-RAY DIFFRACTION	11	K	1082
23	X-RAY DIFFRACTION	12	L	1 - 172
24	X-RAY DIFFRACTION	12	L	1082 - 1153

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