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- PDB-5xcp: Crystal structure of M92A mutant of O-acetyl-L-serine sulfhydryla... -

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Basic information

Entry
Database: PDB / ID: 5xcp
TitleCrystal structure of M92A mutant of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae
ComponentsCysteine synthase
KeywordsTRANSFERASE / pyridoxal phosphate binding / cysteine synthase activity / O-acetylserine (thiol)-lyase / Interacts with Serine acetyl transferase
Function / homology
Function and homology information


cysteine synthase / L-cysteine desulfhydrase activity / cysteine synthase activity / cysteine biosynthetic process from serine / cytoplasm
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 speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.043 Å
AuthorsAbhishek, K. / Kumaran, S.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Molecular Mechanism of Selective Substrate Engagement and Inhibitor Dis-engagement of Cysteine Synthase.
Authors: Kaushik, A. / Rahisuddin, R. / Saini, N. / Singh, R.P. / Kaur, R. / Kaul, S. / Kumaran, S.
History
DepositionMar 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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
X: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)37,1441
Polymers37,1441
Non-polymers00
Water54030
1
X: Cysteine synthase

X: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)74,2892
Polymers74,2892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area3520 Å2
ΔGint-16 kcal/mol
Surface area22820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.390, 112.390, 45.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Cysteine synthase / / CSase / O-acetylserine (thiol)-lyase / OAS-TL / O-acetylserine sulfhydrylase


Mass: 37144.273 Da / Num. of mol.: 1 / Mutation: M92A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: cysK, HI_1103 / Plasmid: pET28A / Details (production host): N-terminal Histag
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P45040, cysteine synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 1.94 Å3/Da / Density % sol: 36.59 % / Description: triangle shaped
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 100mM Hepes buffer pH7.4, 1.4M sodium citrate / PH range: 7.4-7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.514 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.491
ReflectionResolution: 2→19.8 Å / Num. obs: 18182 / % possible obs: 97 % / Redundancy: 7.9 % / Biso Wilson estimate: 16 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.048 / Net I/av σ(I): 9.8 / Net I/σ(I): 34
Reflection shellResolution: 2→2.1 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.084 / Mean I/σ(I) obs: 8.7 / Num. unique obs: 2308 / % possible all: 85.4

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HO1

4ho1


Resolution: 2.043→19 Å / Cross valid method: FREE R-VALUE / σ(F): 2.04 / Phase error: 16.61
RfactorNum. reflection% reflection
Rfree0.1683 928 5.1 %
Rwork0.1507 --
obs0.1525 18182 99.44 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Bsol: 33.994 Å2 / ksol: 0.384 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7525 Å2-0 Å20 Å2
2---2.7525 Å20 Å2
3---5.5049 Å2
Refinement stepCycle: LAST / Resolution: 2.043→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 0 30 2315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082319
X-RAY DIFFRACTIONf_angle_d1.1793151
X-RAY DIFFRACTIONf_dihedral_angle_d14.364848
X-RAY DIFFRACTIONf_chiral_restr0.072376
X-RAY DIFFRACTIONf_plane_restr0.005406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0483-2.10360.19111350.19282556X-RAY DIFFRACTION95
2.1036-2.16530.19191870.19392545X-RAY DIFFRACTION93
2.1653-2.2350.19461050.18132588X-RAY DIFFRACTION96
2.235-2.31470.15891210.17582537X-RAY DIFFRACTION95
2.3147-2.40710.22191600.17692520X-RAY DIFFRACTION94
2.4071-2.51620.19671140.17752597X-RAY DIFFRACTION96
2.5162-2.64830.18721500.18112544X-RAY DIFFRACTION94
2.6483-2.81340.17671230.1732585X-RAY DIFFRACTION95
2.8134-3.02920.16411480.15832559X-RAY DIFFRACTION95
3.0292-3.33150.15651220.14292551X-RAY DIFFRACTION95
3.3315-3.80780.15641580.12722555X-RAY DIFFRACTION94
3.8078-4.77570.14351340.10062563X-RAY DIFFRACTION95
4.7757-15.89480.16021340.13992564X-RAY DIFFRACTION95

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