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- PDB-4oyh: Structure of Bacillus subtilis MobB -

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Basic information

Entry
Database: PDB / ID: 4oyh
TitleStructure of Bacillus subtilis MobB
ComponentsMolybdopterin-guanine dinucleotide biosynthesis protein B
KeywordsBIOSYNTHETIC PROTEIN / Molybdenum / MobB
Function / homology
Function and homology information


Mo-molybdopterin cofactor biosynthetic process / GTP binding
Similarity search - Function
Molybdopterin-guanine dinucleotide biosynthesis protein B (MobB) domain / Molybdopterin guanine dinucleotide synthesis protein B / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Molybdopterin-guanine dinucleotide biosynthesis protein B
Similarity search - Component
Biological speciesBacillus subtilis subsp. spizizenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.409 Å
AuthorsKim, D. / Choe, J.
CitationJournal: To Be Published
Title: Bacillus subtilis MobB
Authors: Kim, D. / Choe, J.
History
DepositionFeb 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist / struct_keywords / symmetry
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text / _symmetry.Int_Tables_number

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Molybdopterin-guanine dinucleotide biosynthesis protein B
B: Molybdopterin-guanine dinucleotide biosynthesis protein B
C: Molybdopterin-guanine dinucleotide biosynthesis protein B
D: Molybdopterin-guanine dinucleotide biosynthesis protein B
E: Molybdopterin-guanine dinucleotide biosynthesis protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,80618
Polymers97,5575
Non-polymers1,24913
Water3,927218
1
A: Molybdopterin-guanine dinucleotide biosynthesis protein B
hetero molecules

A: Molybdopterin-guanine dinucleotide biosynthesis protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,79110
Polymers39,0232
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area5470 Å2
ΔGint-131 kcal/mol
Surface area14490 Å2
MethodPISA
2
B: Molybdopterin-guanine dinucleotide biosynthesis protein B
E: Molybdopterin-guanine dinucleotide biosynthesis protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4076
Polymers39,0232
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-92 kcal/mol
Surface area15070 Å2
MethodPISA
3
C: Molybdopterin-guanine dinucleotide biosynthesis protein B
D: Molybdopterin-guanine dinucleotide biosynthesis protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5037
Polymers39,0232
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-99 kcal/mol
Surface area14910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.528, 42.107, 93.620
Angle α, β, γ (deg.)90.00, 100.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Molybdopterin-guanine dinucleotide biosynthesis protein B


Mass: 19511.389 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. spizizenii (strain ATCC 23059 / NRRL B-14472 / W23) (bacteria)
Gene: BSUW23_07340,mobB / Production host: Escherichia coli (E. coli) / References: UniProt: E0U3U4
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG3350 0.4M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 33530 / % possible obs: 98.8 % / Redundancy: 25 % / Net I/σ(I): 9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 2.409→29.271 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3034 1682 5.02 %
Rwork0.2105 --
obs0.2152 33512 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.409→29.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5904 0 65 218 6187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146057
X-RAY DIFFRACTIONf_angle_d1.5598196
X-RAY DIFFRACTIONf_dihedral_angle_d20.4122231
X-RAY DIFFRACTIONf_chiral_restr0.06954
X-RAY DIFFRACTIONf_plane_restr0.0071028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4094-2.48020.41381500.29482580X-RAY DIFFRACTION96
2.4802-2.56020.36251260.25632622X-RAY DIFFRACTION100
2.5602-2.65170.34811310.24552674X-RAY DIFFRACTION100
2.6517-2.75780.3671380.23092674X-RAY DIFFRACTION100
2.7578-2.88320.33091480.24222630X-RAY DIFFRACTION100
2.8832-3.0350.33031440.2332717X-RAY DIFFRACTION100
3.035-3.2250.3271370.21792682X-RAY DIFFRACTION100
3.225-3.47360.31161300.20982682X-RAY DIFFRACTION100
3.4736-3.82250.2911370.19682704X-RAY DIFFRACTION99
3.8225-4.3740.26251410.17612650X-RAY DIFFRACTION99
4.374-5.50480.27631580.17342669X-RAY DIFFRACTION98
5.5048-29.27290.2861420.23342546X-RAY DIFFRACTION90

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