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- PDB-4nkr: The Crystal structure of Bacillus subtilis MobB -

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Basic information

Entry
Database: PDB / ID: 4nkr
TitleThe Crystal structure of Bacillus subtilis MobB
ComponentsMolybdopterin-guanine dinucleotide biosynthesis protein B
KeywordsUNKNOWN FUNCTION / P-loop / Walker A motif / nucleotide binding / GTP / phosphate binding / Cytosol
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 / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsChoe, J. / Kim, D. / Choi, S. / Kim, H.
CitationJournal: TO BE PUBLISHED
Title: Insight into the Role of E.coli MobB in Molybdenum Cofactor Biosynthesis based on the high resolution crystal structure
Authors: Mcluskey, K.
History
DepositionNov 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: 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)93,65918
Polymers92,4105
Non-polymers1,24913
Water4,125229
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)37,5418
Polymers36,9642
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area5730 Å2
ΔGint-129 kcal/mol
Surface area14590 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)37,4447
Polymers36,9642
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-94 kcal/mol
Surface area15990 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)37,4447
Polymers36,9642
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-104 kcal/mol
Surface area14960 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: 18482.086 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. spizizenii (bacteria)
Strain: ATCC 23059 / NRRL B-14472 / W23 / 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.: 229 / 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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 23% PEG 3350, 0.4M Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: PHILLIPS / Detector: DIFFRACTOMETER / Date: Oct 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 31830 / % possible obs: 98.8 %
Reflection shellHighest resolution: 2 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→29.27 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.866 / SU B: 11.044 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R: 0.542 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32077 1682 5 %RANDOM
Rwork0.22669 ---
obs0.23146 31830 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.149 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.01 Å2
2---0.02 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.41→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5991 0 65 229 6285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0196146
X-RAY DIFFRACTIONr_bond_other_d0.0020.026063
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9848315
X-RAY DIFFRACTIONr_angle_other_deg0.824313950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7775748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31324.779272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.38151114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1861530
X-RAY DIFFRACTIONr_chiral_restr0.1010.2977
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026747
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021323
LS refinement shellResolution: 2.41→2.472 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 131 -
Rwork0.312 2260 -
obs--95.45 %

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