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- PDB-1gun: MopII from Clostridium pasteurianum complexed with molybdate (partial) -

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Basic information

Entry
Database: PDB / ID: 1gun
TitleMopII from Clostridium pasteurianum complexed with molybdate (partial)
ComponentsMOLYBDATE BINDING PROTEIN II
KeywordsTRANSPORT PROTEIN / MOLBINDIN / MOLYBDATE BINDING / MOP
Function / homology
Function and homology information


molybdate ion transport
Similarity search - Function
Mop domain profile. / Molybdenum-pterin binding domain / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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 2, 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 / pdbx_struct_conn_angle / struct_conn / 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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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)43,46316
Polymers42,1046
Non-polymers1,36010
Water2,954164
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)43,46316
Polymers42,1046
Non-polymers1,36010
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area19980 Å2
ΔGint-168.7 kcal/mol
Surface area14000 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)43,46316
Polymers42,1046
Non-polymers1,36010
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area20130 Å2
ΔGint-166.1 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.810, 78.380, 95.240
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2022-

HOH

21A-2040-

HOH

31C-2015-

HOH

41D-2017-

HOH

51D-2037-

HOH

61F-2021-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.460396, -0.836396, -0.297452), (0.838776, -0.519585, 0.162746), (-0.290671, -0.174568, 0.940764)1.424, -2.285, 0.276
2given(-0.431745, 0.853971, -0.290395), (-0.854621, -0.490255, -0.171093), (-0.288476, 0.174309, 0.941487)-1.311, -2.453, -0.301
3given(-0.999999, 0.000758, -0.001366), (-0.000757, -1, -0.00031), (-0.001366, -0.000309, 0.999999)-0.012, -0.077, 47.64
4given(0.459381, 0.837043, -0.297202), (-0.838102, 0.519292, 0.167097), (0.294202, 0.172324, 0.94008)-1.42, 2.202, 47.893
5given(0.432542, -0.853649, -0.290157), (0.853517, 0.491391, -0.173332), (0.290545, -0.172681, 0.941151)1.316, 2.364, 47.345

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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 / Molybdate


Mass: 159.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: MoO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 7.6
Details: 95 MM HEPES PH 7.5, 27% POLYETHYLENE GLYCOL 400, 5% GLYCEROL, 190 MM CACL2
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 293 unknown / Method: vapor diffusion, hanging drop
Details: Harrison, J.A., (2001) Acta Crystallogr., D57, 1715.
pH: 7.5
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: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2001 / Details: MIRRORS
RadiationMonochromator: SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.83→20 Å / Num. obs: 36043 / % possible obs: 97.4 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.7
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 3.7 / % possible all: 98.8
Reflection
*PLUS
Num. measured all: 206409
Reflection shell
*PLUS
% possible obs: 98.8 %

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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: 1.83→19.61 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.26 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.139 / 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
Rfree0.248 1815 5 %RANDOM
Rwork0.215 ---
obs0.216 34219 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: 1.83→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 42 164 3092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222933
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.90823954
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_restr0.4740.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021914
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.3853
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.5252
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.3109
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.535
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1761.51977
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.08423192
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7723956
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.4544.5759
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: 1.83→1.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.329 121
Rwork0.285 2518
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2476 / Rfactor Rwork: 0.2147
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.567 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.9
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg9.2
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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