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- PDB-1guo: MopII from Clostridium pasteurianum complexed with molybdate -

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Basic information

Entry
Database: PDB / ID: 1guo
TitleMopII from Clostridium pasteurianum complexed with molybdate
ComponentsMOLYBDATE BINDING PROTEIN II
KeywordsTRANSPORT PROTEIN / MOLYBDATE BINDING / MOP / MOLYBDENUM
Function / homology
Function and homology information


molybdate ion transport
Similarity search - Function
Molybdenum-pterin binding domain / Mop domain profile. / Transport-associated OB, type 1 / TOBE domain / Molybdate/tungstate binding, C-terminal / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
MOLYBDATE ION / Molybdenum-pterin-binding protein 2
Similarity search - Component
Biological speciesCLOSTRIDIUM PASTEURIANUM (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSchuettelkopf, A.W. / Harrison, J.A. / Hunter, W.N.
CitationJournal: 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
DepositionJan 28, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2002Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2May 16, 2012Group: Other
Revision 1.3Dec 13, 2023Group: 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,38314
Polymers42,1046
Non-polymers1,2808
Water23413
1
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


Theoretical massNumber of molelcules
Total (without water)43,38314
Polymers42,1046
Non-polymers1,2808
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area19530 Å2
ΔGint-136.2 kcal/mol
Surface area13390 Å2
MethodPISA
2
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


Theoretical massNumber of molelcules
Total (without water)43,38314
Polymers42,1046
Non-polymers1,2808
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area19540 Å2
ΔGint-134.3 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.144, 77.764, 93.494
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-2002-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.466575, -0.840483, -0.275494), (0.840572, -0.518274, 0.157576), (-0.275221, -0.158051, 0.9483)1.354, -2.379, 0.186
2given(-0.441134, 0.856146, -0.269101), (-0.855819, -0.491576, -0.161018), (-0.270138, 0.159271, 0.949557)-1.337, -2.537, -0.306
3given(-0.99999, -0.003288, -0.003034), (0.003279, -0.99999, 0.003133), (-0.003045, 0.003123, 0.99999)-0.09, -0.056, 46.728
4given(0.467429, 0.840146, -0.275073), (-0.841727, 0.51807, 0.151984), (0.270196, 0.160495, 0.949334)-1.439, 2.3, 46.976
5given(0.441898, -0.856238, -0.267548), (0.855536, 0.491956, -0.161362), (0.269786, -0.157591, 0.949937)1.303, 2.451, 46.441

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Components

#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-MOO / MOLYBDATE ION / MOLYBDATE


Mass: 159.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: MoO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 %
Crystal growpH: 7.6
Details: 95 MM HEPES PH 7.5, 27% POLYETHYLENE GLYCOL 400,5% GLYCEROL, 190 MM CACL2 WITH 1.6 MM NA2MOO4 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
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mM1reservoirfivefold molar excess relative to MopIINa2WO4
295 mMHEPES1reservoirpH7.5
326.6 %(w/v)PEG4001reservoir
45 %(w/v)glycerol1reservoir
5190 mM1reservoirCaCl2
630 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jul 15, 2001 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 10097 / % possible obs: 98.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 27.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 4.4 / % possible all: 89.2
Reflection
*PLUS
Num. measured all: 173881 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 89.2 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GUG

1gug


Resolution: 2.5→29.88 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.92 / SU B: 13.65 / SU ML: 0.31 / Cross valid method: THROUGHOUT / ESU R Free: 0.356 / 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 485 4.8 %RANDOM
Rwork0.21 ---
obs0.212 9610 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 2.5→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2874 0 40 13 2927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222814
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.4981.9943794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.4510.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021854
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2610.3987
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.5236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.3218
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.542
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6561.51950
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21723114
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8983864
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2824.5680
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.287 26
Rwork0.264 497
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 49.92 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.5
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg9.7
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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