PDB-1gug: MopII from Clostridium pasteurianum complexed with tungstate

ID or keywords:

Entry

Database: PDB / ID: 1gug

Title

MopII from Clostridium pasteurianum complexed with tungstate

Components

MOLYBDATE BINDING PROTEIN II

Keywords

MOLYBDATE BINDING 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 /

SYNCHROTRON /

SIRAS / Resolution: 1.6 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 25, 2002	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 8, 2002	Provider: repository / Type: Initial release
Revision 1.1	Apr 18, 2012	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2	May 8, 2024	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 / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	1gug.cif.gz	88.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	1gug_validation.pdf.gz	463.7 KB	Display	wwPDB validaton report
Full document	1gug_full_validation.pdf.gz	464.6 KB	Display
Data in XML	1gug_validation.xml.gz	17.9 KB	Display
Data in CIF	1gug_validation.cif.gz	26.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gu/1gug ftp://data.pdbj.org/pub/pdb/validation_reports/gu/1gug	HTTPS FTP

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Related structure data

Related structure data	1gunC 1guoC 1gusC 1gutC C: citing same article (ref.)
Similar structure data	1guo-1 1gun-1 1gut-d 1guo-2 1gus-d 3m15-d 1fr3-1 6u6n-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

44.2 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

D: MOLYBDATE BINDING PROTEIN II

E: MOLYBDATE BINDING PROTEIN II

F: MOLYBDATE BINDING PROTEIN II

hetero molecules

D: MOLYBDATE BINDING PROTEIN II

E: MOLYBDATE BINDING PROTEIN II

F: MOLYBDATE BINDING PROTEIN II

hetero molecules

defined by software
44.2 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: MOLYBDATE BINDING PROTEIN II

B: MOLYBDATE BINDING PROTEIN II

C: MOLYBDATE BINDING PROTEIN II

hetero molecules

A: MOLYBDATE BINDING PROTEIN II

B: MOLYBDATE BINDING PROTEIN II

C: MOLYBDATE BINDING PROTEIN II

hetero molecules

defined by software
44.2 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	56.373, 78.514, 94.839
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	C-1070- NA
2	1	F-1070- NA
3	1	A-2027- HOH
4	1	A-2049- HOH
5	1	C-2037- HOH
6	1	D-2026- HOH
7	1	D-2046- HOH
8	1	F-2031- 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	ILE	ILE	GLY	GLY	A	A	3 - 11	3 - 11
2	1	ILE	ILE	GLY	GLY	B	B	3 - 11	3 - 11
3	1	ILE	ILE	GLY	GLY	C	C	3 - 11	3 - 11
4	1	ILE	ILE	GLY	GLY	D	D	3 - 11	3 - 11
5	1	ILE	ILE	GLY	GLY	E	E	3 - 11	3 - 11
6	1	ILE	ILE	GLY	GLY	F	F	3 - 11	3 - 11
1	2	VAL	VAL	VAL	VAL	A	A	13 - 26	13 - 26
2	2	VAL	VAL	VAL	VAL	B	B	13 - 26	13 - 26
3	2	VAL	VAL	VAL	VAL	C	C	13 - 26	13 - 26
4	2	VAL	VAL	VAL	VAL	D	D	13 - 26	13 - 26
5	2	VAL	VAL	VAL	VAL	E	E	13 - 26	13 - 26
6	2	VAL	VAL	VAL	VAL	F	F	13 - 26	13 - 26
1	3	ILE	ILE	ILE	ILE	A	A	29	29
2	3	ILE	ILE	ILE	ILE	B	B	29	29
3	3	ILE	ILE	ILE	ILE	C	C	29	29
4	3	ILE	ILE	ILE	ILE	D	D	29	29
5	3	ILE	ILE	ILE	ILE	E	E	29	29
6	3	ILE	ILE	ILE	ILE	F	F	29	29
1	4	ILE	ILE	SER	SER	A	A	35 - 43	35 - 43
2	4	ILE	ILE	SER	SER	B	B	35 - 43	35 - 43
3	4	ILE	ILE	SER	SER	C	C	35 - 43	35 - 43
4	4	ILE	ILE	SER	SER	D	D	35 - 43	35 - 43
5	4	ILE	ILE	SER	SER	E	E	35 - 43	35 - 43
6	4	ILE	ILE	SER	SER	F	F	35 - 43	35 - 43
1	5	GLU	GLU	ILE	ILE	A	A	45 - 66	45 - 66
2	5	GLU	GLU	ILE	ILE	B	B	45 - 66	45 - 66
3	5	GLU	GLU	ILE	ILE	C	C	45 - 66	45 - 66
4	5	GLU	GLU	ILE	ILE	D	D	45 - 66	45 - 66
5	5	GLU	GLU	ILE	ILE	E	E	45 - 66	45 - 66
6	5	GLU	GLU	ILE	ILE	F	F	45 - 66	45 - 66

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.469142, 0.841996, 0.266362), (-0.842577, -0.517099, 0.150574), (0.264518, -0.15379, 0.952039)	72.339, 61.761, -12.969
2	given	(-0.440421, -0.859581, 0.259132), (0.857536, -0.488229, -0.162064), (0.265823, 0.150839, 0.952148)	-16.217, 93.96, 3.313
3	given	(-0.999997, -0.002481, -0.000351), (0.002482, -0.999997, -0.000883), (-0.000348, -0.000884, 1)	56.258, 100.039, -47.351
4	given	(0.471295, -0.8407, 0.266656), (0.841472, 0.519178, 0.149597), (-0.264207, 0.153879, 0.952111)	-16.01, 38.079, -60.364
5	given	(0.439881, 0.859831, 0.259219), (-0.858014, 0.487609, -0.161399), (-0.265173, -0.151417, 0.952237)	72.555, 6.039, -44.137

#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-WO4 / TUNGSTATE(VI)ION Mass: 247.838 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: WO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.5 Å³/Da / Density % sol: 50 %

Crystal grow

pH: 7.6
Details: 95 MM HEPES PH 7.5, 27% POLYETHYLENE GLYCOL 400, 5% GLYCEROL, 190 MM CACL2 WITH 1.6 MM NA2WO4 IN THE DROP

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	Details	Chemical formula
1	8 mM		1	reservoir	fivefold molar excess relative to MopII	Na2WO4
2	95 mM	HEPES	1	reservoir	pH7.5
3	26.6 %(w/v)	PEG400	1	reservoir
4	5 %(w/v)	glycerol	1	reservoir
5	190 mM		1	reservoir		CaCl2
6	30 mg/ml	protein	1	drop

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
Detector	Type: ADSC CCD / Detector: CCD / Date: Feb 15, 2001 / Details: MIRRORS
Radiation	Monochromator: SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.87 Å / Relative weight: 1
Reflection	Resolution: 1.6→20 Å / Num. obs: 53578 / % possible obs: 93.6 % / Redundancy: 1.9 % / R_merge(I) obs: 0.068 / Net I/σ(I): 14.7
Reflection shell	Resolution: 1.6→1.66 Å / Redundancy: 1.7 % / R_merge(I) obs: 0.264 / Mean I/σ(I) obs: 4.3 / % possible all: 90.4
Reflection	PLUS Num. measured all*: 405754
Reflection shell	PLUS % possible obs*: 90.4 %

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Processing

Software

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

Refinement

Method to determine structure:

SIRAS / Resolution: 1.6→19.61 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.945 / SU B: 1.319 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE DATA SET WAS ORIGINALLY PROCESSED/SCALED IN AN ORTHORHOMBIC SPACE GROUP, BUT COULD NOT BE REFINED WITH THE ADDITIONAL CRYSTALLOGRAPHIC SYMMETRY.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18254	2685	5 %	RANDOM
R_work	0.15433	-	-	-
obs	0.1557	50781	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

Displacement parameters

B_iso mean: 19.277 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.36 Å²	0 Å²	-0.02 Å²
2-	-	-0.24 Å²	0 Å²
3-	-	-	-1.12 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→19.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2886	0	44	244	3174

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	2912
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg
X-RAY DIFFRACTION	r_angle_other_deg	1.342	2.021	3910
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	0.09	0.2	528
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1902
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.3	905
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	0.161	0.5	220
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	0.235	0.3	149
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.122	0.5	44
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	0.765	1.5	1968
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.398	2	3168
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.463	3	944
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.461	4.5	742
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	69	tight positional	0.04	0.05
2	B	69	tight positional	0.03	0.05
3	C	69	tight positional	0.03	0.05
4	D	69	tight positional	0.04	0.05
5	E	69	tight positional	0.04	0.05
6	F	69	tight positional	0.03	0.05
1	A	181	medium positional	0.1	0.5
2	B	181	medium positional	0.1	0.5
3	C	181	medium positional	0.07	0.5
4	D	181	medium positional	0.1	0.5
5	E	181	medium positional	0.09	0.5
6	F	181	medium positional	0.07	0.5
1	A	148	loose positional	0.21	5
2	B	148	loose positional	0.24	5
3	C	148	loose positional	0.19	5
4	D	148	loose positional	0.27	5
5	E	148	loose positional	0.22	5
6	F	148	loose positional	0.36	5
1	A	69	tight thermal	0.28	0.5
2	B	69	tight thermal	0.19	0.5
3	C	69	tight thermal	0.19	0.5
4	D	69	tight thermal	0.27	0.5
5	E	69	tight thermal	0.18	0.5
6	F	69	tight thermal	0.16	0.5
1	A	181	medium thermal	1.59	2
2	B	181	medium thermal	0.94	2
3	C	181	medium thermal	0.89	2
4	D	181	medium thermal	1.6	2
5	E	181	medium thermal	0.88	2
6	F	181	medium thermal	0.8	2
1	A	148	loose thermal	1.74	10
2	B	148	loose thermal	1.14	10
3	C	148	loose thermal	1.25	10
4	D	148	loose thermal	1.79	10
5	E	148	loose thermal	1.16	10
6	F	148	loose thermal	1.05	10

LS refinement shell

Resolution: 1.6→1.641 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.16	179
R_work	0.165	3682

Software

*PLUS

Name: REFMAC / Version: 5 / Classification: refinement

Refinement

*PLUS

R_factor obs: 0.1557

Solvent computation

*PLUS

Displacement parameters

*PLUS

B_iso mean: 19.277 Å²

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	p_bond_d	0.013
X-RAY DIFFRACTION	p_angle_d
X-RAY DIFFRACTION	p_angle_deg	1.3
X-RAY DIFFRACTION	p_dihedral_angle_d
X-RAY DIFFRACTION	p_dihedral_angle_deg	8.2
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

LS refinement shell

*PLUS

R_factor R_free: 0.16

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