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- PDB-5xcn: Crystal structure of M120A mutant of O-acetyl-L-serine sulfahydry... -

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Basic information

Entry
Database: PDB / ID: 5xcn
TitleCrystal structure of M120A mutant of O-acetyl-L-serine sulfahydrylase from Haemophilus influenzae
ComponentsCysteine synthase
KeywordsTRANSFERASE / Pyridoxal phosphate binding / cysteine synthase activity / L-cysteine desulfhydrase activity / transferase activity / serine acetyl transferase interacting protein
Function / homology
Function and homology information


L-cysteine desulfhydrase activity / cysteine synthase / 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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold ...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 / 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 speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.69 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 1.1Sep 9, 2020Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Revision 1.2Mar 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 1.3Nov 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
Water4,234235
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 area4270 Å2
ΔGint-21 kcal/mol
Surface area22450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.273, 112.273, 46.092
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: M120A
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


Mass: 18.015 Da / Num. of mol.: 235 / 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: 1.96 Å3/Da / Density % sol: 37.48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100mM HEPES buffer at pH7.5, 1.3M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.69→28.07 Å / Num. obs: 30261 / % possible obs: 100 % / Redundancy: 4.8 % / Biso Wilson estimate: 23 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.9

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HO1

4ho1


Resolution: 1.69→27 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.81
RfactorNum. reflection% reflectionSelection details
Rfree0.1969 1520 5.02 %5%
Rwork0.1664 ---
obs0.1679 30253 94.14 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Bsol: 47.751 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.7171 Å2-0 Å20 Å2
2---4.7171 Å20 Å2
3---9.4343 Å2
Refinement stepCycle: LAST / Resolution: 1.69→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2303 0 0 235 2538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072354
X-RAY DIFFRACTIONf_angle_d1.1053204
X-RAY DIFFRACTIONf_dihedral_angle_d12.904863
X-RAY DIFFRACTIONf_chiral_restr0.074385
X-RAY DIFFRACTIONf_plane_restr0.005410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6944-1.74910.45331330.39172417X-RAY DIFFRACTION87
1.7491-1.81160.30691360.28632675X-RAY DIFFRACTION97
1.8116-1.88410.25231310.21082669X-RAY DIFFRACTION96
1.8841-1.96990.19451290.17422617X-RAY DIFFRACTION95
1.9699-2.07370.22341490.16352580X-RAY DIFFRACTION94
2.0737-2.20360.18961430.1582552X-RAY DIFFRACTION92
2.2036-2.37360.19541300.1562565X-RAY DIFFRACTION93
2.3736-2.61240.18871500.15442613X-RAY DIFFRACTION95
2.6124-2.99010.19041430.16392672X-RAY DIFFRACTION96
2.9901-3.76590.21031320.14992708X-RAY DIFFRACTION96
3.7659-29.05760.15481440.15132665X-RAY DIFFRACTION93

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