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- PDB-5jjc: Crystal Structure of double mutant (Q96A-Y125A) O-Acetyl Serine S... -

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Basic information

Entry
Database: PDB / ID: 5jjc
TitleCrystal Structure of double mutant (Q96A-Y125A) O-Acetyl Serine Sulfhydralase from Brucella abortus
ComponentsCysteine synthase
KeywordsTRANSFERASE / cysteine synthase
Function / homology
Function and homology information


cysteine biosynthetic process from serine / transferase activity, transferring alkyl or aryl (other than methyl) groups
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 / 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 speciesBrucella abortus S19 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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 23, 2016Deposition site: PDBJ / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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)147,2744
Polymers147,2744
Non-polymers00
Water17,096949
1
A: Cysteine synthase
C: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)73,6372
Polymers73,6372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-25 kcal/mol
Surface area24160 Å2
MethodPISA
2
B: Cysteine synthase
D: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)73,6372
Polymers73,6372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-25 kcal/mol
Surface area24020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.820, 104.820, 242.041
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: 36818.457 Da / Num. of mol.: 4 / Mutation: Q96A, Y125A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus S19 (bacteria) / Strain: S19 / Gene: BAbS19_I09950 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0F6AQU1, cysteine synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 949 / 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: 52.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.2
Details: sodium phosphate monobasic monohydrate, potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.01→90.78 Å / Num. obs: 98795 / % possible obs: 99 % / Redundancy: 4.4 % / Net I/σ(I): 24.7
Reflection shellResolution: 2.01→2.08 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JIS

5jis


Resolution: 2.01→33.971 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.71 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 4925 4.99 %RANDOM
Rwork0.1682 ---
obs0.1702 98757 99.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→33.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9996 0 0 949 10945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910184
X-RAY DIFFRACTIONf_angle_d1.17713831
X-RAY DIFFRACTIONf_dihedral_angle_d14.6213717
X-RAY DIFFRACTIONf_chiral_restr0.051569
X-RAY DIFFRACTIONf_plane_restr0.0051821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0099-2.03280.23741700.17553069X-RAY DIFFRACTION97
2.0328-2.05670.22341540.16943191X-RAY DIFFRACTION100
2.0567-2.08180.23731560.16643096X-RAY DIFFRACTION100
2.0818-2.10810.19571420.16233186X-RAY DIFFRACTION100
2.1081-2.13580.23811700.16793164X-RAY DIFFRACTION100
2.1358-2.16510.21151590.15913146X-RAY DIFFRACTION100
2.1651-2.1960.21181570.16933121X-RAY DIFFRACTION100
2.196-2.22880.24491830.16873178X-RAY DIFFRACTION100
2.2288-2.26360.21861800.17033064X-RAY DIFFRACTION100
2.2636-2.30070.21321530.17023189X-RAY DIFFRACTION100
2.3007-2.34040.24651640.16723106X-RAY DIFFRACTION99
2.3404-2.38290.25141380.17633201X-RAY DIFFRACTION100
2.3829-2.42880.20321300.17713142X-RAY DIFFRACTION100
2.4288-2.47830.20951690.16663122X-RAY DIFFRACTION99
2.4783-2.53220.22471850.17463114X-RAY DIFFRACTION100
2.5322-2.59110.22951800.17083132X-RAY DIFFRACTION99
2.5911-2.65580.26911720.17653107X-RAY DIFFRACTION99
2.6558-2.72760.23371630.18073154X-RAY DIFFRACTION99
2.7276-2.80790.21141890.18113090X-RAY DIFFRACTION99
2.8079-2.89840.23141760.1933153X-RAY DIFFRACTION99
2.8984-3.0020.25541360.19953108X-RAY DIFFRACTION99
3.002-3.12210.23081990.20023088X-RAY DIFFRACTION99
3.1221-3.26410.22931560.1793139X-RAY DIFFRACTION99
3.2641-3.4360.21991510.17813127X-RAY DIFFRACTION99
3.436-3.6510.19521550.16283113X-RAY DIFFRACTION99
3.651-3.93260.1651490.14153111X-RAY DIFFRACTION98
3.9326-4.32760.16431740.13693096X-RAY DIFFRACTION98
4.3276-4.95220.15781620.13953108X-RAY DIFFRACTION98
4.9522-6.23290.18491590.16993099X-RAY DIFFRACTION98
6.2329-33.97560.18941940.1713118X-RAY DIFFRACTION98

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