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- PDB-2egu: Crystal structure of O-acetylserine sulfhydrase from Geobacillus ... -

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Basic information

Entry
Database: PDB / ID: 2egu
TitleCrystal structure of O-acetylserine sulfhydrase from Geobacillus kaustophilus HTA426
ComponentsCysteine synthase
KeywordsTRANSFERASE / O-acetylserine sulfhydrase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine
Similarity search - Function
Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRehse, P.H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of O-acetylserine sulfhydrase from Geobacillus kaustophilus HTA426
Authors: Rehse, P.H. / Yokoyama, S.
History
DepositionMar 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)32,5551
Polymers32,5551
Non-polymers00
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cysteine synthase

A: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)65,1112
Polymers65,1112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area4740 Å2
ΔGint-20 kcal/mol
Surface area23290 Å2
MethodPISA, PQS
3
A: Cysteine synthase

A: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)65,1112
Polymers65,1112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1530 Å2
ΔGint-7 kcal/mol
Surface area26500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.250, 72.250, 127.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-354-

HOH

21A-539-

HOH

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Components

#1: Protein Cysteine synthase / / O-acetyl-L-serine sulfhydrylase


Mass: 32555.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Plasmid: pET-15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL26-codonPlus (DE3)-RIL / References: UniProt: Q5L3S8, cysteine synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 100mM MES-NaOH, 50mM MgCl2, 27.5% PEG 4000, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.9794 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 16, 2006 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 27260 / Num. obs: 27236 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 36.86
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 5.22 / Num. unique all: 2654 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z7W.pdb

1z7w


Resolution: 1.9→39.81 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1314 4.8 %random
Rwork0.201 ---
obs0.201 26955 98.8 %-
all-27236 --
Solvent computationBsol: 35.998 Å2
Displacement parametersBiso mean: 28.574 Å2
Baniso -1Baniso -2Baniso -3
1--1.982 Å20 Å20 Å2
2---1.982 Å20 Å2
3---3.963 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→39.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 0 246 2252
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0063981.5
X-RAY DIFFRACTIONc_angle_deg1.353352
X-RAY DIFFRACTIONc_dihedral_angle_d23.074422
X-RAY DIFFRACTIONc_improper_angle_d0.940172.5
LS refinement shellResolution: 1.9→1.97 Å
RfactorNum. reflection% reflection
Rfree0.2347 128 -
Rwork0.2268 --
obs-2539 0.9545 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4lig.param

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