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- PDB-5jis: The Crystal Structure of O-acetyl serine sulfhydralase from Bruce... -

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Basic information

Entry
Database: PDB / ID: 5jis
TitleThe Crystal Structure of O-acetyl serine sulfhydralase from Brucella abortus
ComponentsCysteine synthase
KeywordsTRANSFERASE
Function / homology
Function and homology information


transferase activity, transferring alkyl or aryl (other than methyl) groups / L-cysteine biosynthetic process from L-serine
Similarity search - Function
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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBrucella abortus S19 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDharavath, S. / Gourinath, S.
CitationJournal: Biochem. J. / Year: 2017
Title: Structure-based mutational studies of O-acetylserine sulfhydrylase reveal the reason for the loss of cysteine synthase complex formation in Brucella abortus
Authors: Dharavath, S. / Raj, I. / Gourinath, S.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine synthase
B: Cysteine synthase
C: Cysteine synthase
D: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)152,1554
Polymers152,1554
Non-polymers00
Water7,981443
1
A: Cysteine synthase
D: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)76,0772
Polymers76,0772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-29 kcal/mol
Surface area24500 Å2
MethodPISA
2
B: Cysteine synthase
C: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)76,0772
Polymers76,0772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-26 kcal/mol
Surface area24720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.794, 104.794, 241.512
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Cysteine synthase / O-acetyl serine sulfhydralase


Mass: 38038.742 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus S19 (bacteria) / Strain: S19 / Gene: BAbS19_I09950 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F6AQU1, cysteine synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.59 Å3/Da / Density % sol: 52.48 % / Description: Diamond shaped
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.5 / Details: sodium cacodylate, potassium bromide, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 75389 / % possible obs: 99.9 % / Redundancy: 4.7 % / Net I/σ(I): 12.41
Reflection shellResolution: 2.2→2.24 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1o58

1o58


Resolution: 2.2→40.068 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.857 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22551 3646 4.9 %RANDOM
Rwork0.18399 ---
obs0.18604 70554 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.005 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.09 Å20 Å2
2---0.17 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10182 0 0 443 10625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910387
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210005
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.97914105
X-RAY DIFFRACTIONr_angle_other_deg0.951322980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12651340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74824.405454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.066151683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7891572
X-RAY DIFFRACTIONr_chiral_restr0.0790.21591
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111976
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022304
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2492.4625363
X-RAY DIFFRACTIONr_mcbond_other1.2492.4625362
X-RAY DIFFRACTIONr_mcangle_it2.0733.6816696
X-RAY DIFFRACTIONr_mcangle_other2.0733.6816697
X-RAY DIFFRACTIONr_scbond_it1.4852.7455024
X-RAY DIFFRACTIONr_scbond_other1.4842.7445022
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5214.0267407
X-RAY DIFFRACTIONr_long_range_B_refined4.04819.72311681
X-RAY DIFFRACTIONr_long_range_B_other4.04219.71611665
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 272 -
Rwork0.185 5012 -
obs--94.92 %

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