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- PDB-1twj: Crystal Structure of B. subtilis PurS P21 Crystal Form -

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Basic information

Entry
Database: PDB / ID: 1twj
TitleCrystal Structure of B. subtilis PurS P21 Crystal Form
ComponentsHypothetical UPF0062 protein yexA
KeywordsFormylglycinamide Synthetase / PurS / FGAM
Function / homology
Function and homology information


phosphoribosylformylglycinamidine synthase / phosphoribosylformylglycinamidine synthase activity / 'de novo' IMP biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Mth169; Chain: A , / Phosphoribosylformylglycinamidine synthase subunit PurS / Phosphoribosylformylglycinamidine synthase subunit PurS / Phosphoribosylformylglycinamidine (FGAM) synthase / Phosphoribosylformylglycinamidine synthase subunit PurS-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoribosylformylglycinamidine synthase subunit PurS
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAnand, R. / Ealick, S.E. / Hoskins, A.A. / Stubbe, J.
CitationJournal: Biochemistry / Year: 2004
Title: A Model for the Bacillus subtilis Formylglycinamide Ribonucleotide Amidotransferase Multiprotein Complex
Authors: Anand, R. / Hoskins, A.A. / Bennett, E.M. / Sintchak, M.D. / Stubbe, J. / Ealick, S.E.
History
DepositionJul 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical UPF0062 protein yexA
B: Hypothetical UPF0062 protein yexA
C: Hypothetical UPF0062 protein yexA
D: Hypothetical UPF0062 protein yexA


Theoretical massNumber of molelcules
Total (without water)39,0694
Polymers39,0694
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-47 kcal/mol
Surface area15890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.905, 87.955, 52.679
Angle α, β, γ (deg.)90.00, 94.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hypothetical UPF0062 protein yexA / PurS


Mass: 9767.169 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YEXA, BSU06460 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P12049
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 3 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.0M ammonium sulfate, 6% Peg 400, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 23, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 13053 / Num. obs: 13053 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 10
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 5 / Rsym value: 0.318 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1GTD

1gtd


Resolution: 2.5→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.321 666
Rwork0.248 -
all0.251 13053
obs0.249 13053
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 0 0 149 2635
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3

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