PDB-1gus: MopII from Clostridium pasteurianum (apo1)

ID or keywords:

Entry

Database: PDB / ID: 1gus

Title

MopII from Clostridium pasteurianum (apo1)

Components

MOLYBDATE BINDING PROTEIN II

Keywords

TRANSPORT PROTEIN / MOLBINDIN / MOLYBDATE BINDING / MOP

Function / homology

Function and homology information

molybdate ion transport
Similarity search - Function

Biological species

CLOSTRIDIUM PASTEURIANUM (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Schuettelkopf, A.W. / Harrison, J.A. / Hunter, W.N.

Citation

Journal: J.Biol.Chem. / Year: 2002
Title: Passive Acquisition of Ligand by the Mopii Molbindin from Clostridium Pasteurianum: Structures of Apo and Oxyanion-Bound Forms
Authors: Schuettelkopf, A.W. / Harrison, J.A. / Boxer, D.H. / Hunter, W.N.

History

Deposition	Jan 28, 2002	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 8, 2002	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1gus.cif.gz	89.9 KB	Display	PDBx/mmCIF format
PDB format	pdb1gus.ent.gz	70.3 KB	Display	PDB format
PDBx/mmJSON format	1gus.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gu/1gus ftp://data.pdbj.org/pub/pdb/validation_reports/gu/1gus	HTTPS FTP

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Related structure data

Related structure data	1gugSC 1gunC 1guoC 1gutC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1gun-2 1gut-d 1gug-2 1gun-1 1guo-2 1guo-1 1gug-1 6wz3-d 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: MOLYBDATE BINDING PROTEIN II

B: MOLYBDATE BINDING PROTEIN II

C: MOLYBDATE BINDING PROTEIN II

D: MOLYBDATE BINDING PROTEIN II

E: MOLYBDATE BINDING PROTEIN II

F: MOLYBDATE BINDING PROTEIN II

hetero molecules

42.3 kDa, 6 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)	79.080, 82.400, 56.820
Angle α, β, γ (deg.)	90.00, 93.23, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-2005- HOH
2	1	D-2011- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-ID	Component-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	SER	SER	LEU	LEU	A	A	4 - 9	4 - 9
2	1	SER	SER	LEU	LEU	B	B	4 - 9	4 - 9
3	1	SER	SER	LEU	LEU	C	C	4 - 9	4 - 9
4	1	SER	SER	LEU	LEU	D	D	4 - 9	4 - 9
5	1	SER	SER	LEU	LEU	E	E	4 - 9	4 - 9
6	1	SER	SER	LEU	LEU	F	F	4 - 9	4 - 9
1	2	GLY	GLY	GLY	GLY	A	A	11	11
2	2	GLY	GLY	GLY	GLY	B	B	11	11
3	2	GLY	GLY	GLY	GLY	C	C	11	11
4	2	GLY	GLY	GLY	GLY	D	D	11	11
5	2	GLY	GLY	GLY	GLY	E	E	11	11
6	2	GLY	GLY	GLY	GLY	F	F	11	11
1	3	VAL	VAL	LEU	LEU	A	A	13 - 16	13 - 16
2	3	VAL	VAL	LEU	LEU	B	B	13 - 16	13 - 16
3	3	VAL	VAL	LEU	LEU	C	C	13 - 16	13 - 16
4	3	VAL	VAL	LEU	LEU	D	D	13 - 16	13 - 16
5	3	VAL	VAL	LEU	LEU	E	E	13 - 16	13 - 16
6	3	VAL	VAL	LEU	LEU	F	F	13 - 16	13 - 16
1	4	GLY	GLY	VAL	VAL	A	A	19 - 26	19 - 26
2	4	GLY	GLY	VAL	VAL	B	B	19 - 26	19 - 26
3	4	GLY	GLY	VAL	VAL	C	C	19 - 26	19 - 26
4	4	GLY	GLY	VAL	VAL	D	D	19 - 26	19 - 26
5	4	GLY	GLY	VAL	VAL	E	E	19 - 26	19 - 26
6	4	GLY	GLY	VAL	VAL	F	F	19 - 26	19 - 26
1	5	ILE	ILE	ASN	ASN	A	A	29 - 33	29 - 33
2	5	ILE	ILE	ASN	ASN	B	B	29 - 33	29 - 33
3	5	ILE	ILE	ASN	ASN	C	C	29 - 33	29 - 33
4	5	ILE	ILE	ASN	ASN	D	D	29 - 33	29 - 33
5	5	ILE	ILE	ASN	ASN	E	E	29 - 33	29 - 33
6	5	ILE	ILE	ASN	ASN	F	F	29 - 33	29 - 33
1	6	ILE	ILE	VAL	VAL	A	A	35 - 44	35 - 44
2	6	ILE	ILE	VAL	VAL	B	B	35 - 44	35 - 44
3	6	ILE	ILE	VAL	VAL	C	C	35 - 44	35 - 44
4	6	ILE	ILE	VAL	VAL	D	D	35 - 44	35 - 44
5	6	ILE	ILE	VAL	VAL	E	E	35 - 44	35 - 44
6	6	ILE	ILE	VAL	VAL	F	F	35 - 44	35 - 44
1	7	LEU	LEU	VAL	VAL	A	A	47 - 49	47 - 49
2	7	LEU	LEU	VAL	VAL	B	B	47 - 49	47 - 49
3	7	LEU	LEU	VAL	VAL	C	C	47 - 49	47 - 49
4	7	LEU	LEU	VAL	VAL	D	D	47 - 49	47 - 49
5	7	LEU	LEU	VAL	VAL	E	E	47 - 49	47 - 49
6	7	LEU	LEU	VAL	VAL	F	F	47 - 49	47 - 49
1	8	GLY	GLY	VAL	VAL	A	A	52 - 59	52 - 59
2	8	GLY	GLY	VAL	VAL	B	B	52 - 59	52 - 59
3	8	GLY	GLY	VAL	VAL	C	C	52 - 59	52 - 59
4	8	GLY	GLY	VAL	VAL	D	D	52 - 59	52 - 59
5	8	GLY	GLY	VAL	VAL	E	E	52 - 59	52 - 59
6	8	GLY	GLY	VAL	VAL	F	F	52 - 59	52 - 59
1	9	THR	THR	VAL	VAL	A	A	62 - 64	62 - 64
2	9	THR	THR	VAL	VAL	B	B	62 - 64	62 - 64
3	9	THR	THR	VAL	VAL	C	C	62 - 64	62 - 64
4	9	THR	THR	VAL	VAL	D	D	62 - 64	62 - 64
5	9	THR	THR	VAL	VAL	E	E	62 - 64	62 - 64
6	9	THR	THR	VAL	VAL	F	F	62 - 64	62 - 64
1	10	ILE	ILE	LEU	LEU	A	A	66 - 67	66 - 67
2	10	ILE	ILE	LEU	LEU	B	B	66 - 67	66 - 67
3	10	ILE	ILE	LEU	LEU	C	C	66 - 67	66 - 67
4	10	ILE	ILE	LEU	LEU	D	D	66 - 67	66 - 67
5	10	ILE	ILE	LEU	LEU	E	E	66 - 67	66 - 67
6	10	ILE	ILE	LEU	LEU	F	F	66 - 67	66 - 67

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.460322, 0.519161, 0.720122), (-0.518621, -0.501095, 0.692774), (0.720511, -0.692369, 0.038583)	-0.151, 81.65, 0.08
2	given	(0.461251, -0.52046, 0.718588), (0.51864, -0.498963, -0.694297), (0.719903, 0.692934, 0.039784)	-42.442, 40.657, 56.736
3	given	(-0.997704, -0.067595, -0.004112), (-0.067575, 0.98976, 0.125729), (-0.004429, 0.125719, -0.992056)	37.757, -3.819, 79.521
4	given	(-0.496691, 0.54973, -0.671635), (0.572531, -0.37407, -0.729575), (-0.652308, -0.746906, -0.12894)	30.324, 78.102, 89.632
5	given	(-0.427906, -0.48076, -0.765354), (-0.4536, -0.618201, 0.641931), (-0.781757, 0.62185, 0.046459)	76.523, 48.069, 27.704

#1: Protein	MOLYBDATE BINDING PROTEIN II / MOPII Mass: 7017.250 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM PASTEURIANUM (bacteria) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P08854
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal

Density Matthews: 2.2 Å³/Da / Density % sol: 44 %

Crystal grow

pH: 7.6 / Details: 2 M NACL, 10% POLYETHYLENE GLYCOL 6000, pH 7.60

Crystal grow

*PLUS

Temperature: 293 K / pH: 7.5 / Method: vapor diffusion, hanging drop
Details: Harrison, J.A., (2001) Acta Crystallogr., D57, 1715.

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Chemical formula
1	30 mg/ml	protein	1	drop
2	2 M		1	reservoir	NaCl
3	10 %(w/v)	PEG6000	1	reservoir

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
Detector	Type: RIGAKU R-AXIS IV / Date: May 15, 2001 / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.8→25 Å / Num. obs: 33112 / % possible obs: 97.6 % / Redundancy: 1.9 % / R_merge(I) obs: 0.041 / Net I/σ(I): 16.8
Reflection shell	Resolution: 1.8→1.84 Å / Redundancy: 1.7 % / R_merge(I) obs: 0.28 / Mean I/σ(I) obs: 2.6 / % possible all: 93.9
Reflection	PLUS Num. measured all*: 124432
Reflection shell	PLUS % possible obs: 93.9 % / R_merge(I) obs*: 0.28

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Processing

Software

Name	Version	Classification
REFMAC	5	refinement
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1GUG

1gug

Resolution: 1.8→23.77 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.941 / SU B: 2.815 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.217	1662	5 %	RANDOM
R_work	0.179	-	-	-
obs	0.181	31266	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Refinement step

Cycle: LAST / Resolution: 1.8→23.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2886	0	5	311	3202

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.022	2890
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg
X-RAY DIFFRACTION	r_angle_other_deg	2.046	2.011	3883
X-RAY DIFFRACTION	r_dihedral_angle_1_deg
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.145	0.2	531
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1902
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.23	0.3	1271
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.5	509
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.023	0	2
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.15	0.3	22
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.132	0.5	24
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	1.382	1.5	1971
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.367	2	3178
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.911	3	919
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	7.277	4.5	705
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

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	94	tight positional	0.07	0.05
2	B	94	tight positional	0.08	0.05
3	C	94	tight positional	0.08	0.05
4	D	94	tight positional	0.08	0.05
5	E	94	tight positional	0.08	0.05
6	F	94	tight positional	0.08	0.05
1	A	143	medium positional	0.18	0.5
2	B	143	medium positional	0.17	0.5
3	C	143	medium positional	0.17	0.5
4	D	143	medium positional	0.17	0.5
5	E	143	medium positional	0.18	0.5
6	F	143	medium positional	0.17	0.5
1	A	103	loose positional	0.2	5
2	B	103	loose positional	0.18	5
3	C	103	loose positional	0.19	5
4	D	103	loose positional	0.18	5
5	E	103	loose positional	0.2	5
6	F	103	loose positional	0.19	5
1	A	94	tight thermal	0.45	0.5
2	B	94	tight thermal	0.46	0.5
3	C	94	tight thermal	0.45	0.5
4	D	94	tight thermal	0.45	0.5
5	E	94	tight thermal	0.48	0.5
6	F	94	tight thermal	0.42	0.5
1	A	143	medium thermal	1.1	2
2	B	143	medium thermal	0.87	2
3	C	143	medium thermal	1.01	2
4	D	143	medium thermal	1.05	2
5	E	143	medium thermal	0.97	2
6	F	143	medium thermal	0.91	2
1	A	103	loose thermal	1.97	10
2	B	103	loose thermal	1.86	10
3	C	103	loose thermal	2.08	10
4	D	103	loose thermal	2.12	10
5	E	103	loose thermal	1.97	10
6	F	103	loose thermal	1.77	10

LS refinement shell

Resolution: 1.8→1.85 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.333	115
R_work	0.273	2247

Software

*PLUS

Name: REFMAC / Version: 5 / Classification: refinement

Refinement

*PLUS

Solvent computation

*PLUS

Displacement parameters

*PLUS

B_iso mean: 21.942 Å²

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	p_bond_d	0.019
X-RAY DIFFRACTION	p_angle_d
X-RAY DIFFRACTION	p_angle_deg	2
X-RAY DIFFRACTION	p_dihedral_angle_d
X-RAY DIFFRACTION	p_dihedral_angle_deg	8.4
X-RAY DIFFRACTION	p_chiral_restr
X-RAY DIFFRACTION	p_mcbond_it
X-RAY DIFFRACTION	p_scbond_it
X-RAY DIFFRACTION	p_mcangle_it
X-RAY DIFFRACTION	p_scangle_it

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