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- PDB-5xcw: Crystal structure of M92A-M120A double mutant of O-acetyl-L-serin... -

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Basic information

Entry
Database: PDB / ID: 5xcw
TitleCrystal structure of M92A-M120A double mutant of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae
ComponentsCysteine synthase
KeywordsTRANSFERASE / pyridoxal phosphate binding / transferase activity / cysteine synthase activity / Serine acetyl transferase binding protein
Function / homology
Function and homology information


cysteine synthase / cystathionine beta-synthase activity / cysteine synthase activity / L-cysteine desulfhydrase 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: 1.89 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)37,0841
Polymers37,0841
Non-polymers00
Water3,297183
1
X: Cysteine synthase

X: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)74,1682
Polymers74,1682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area4120 Å2
ΔGint-20 kcal/mol
Surface area21980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.546, 112.546, 46.345
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: 37084.156 Da / Num. of mol.: 1 / Mutation: M92A, 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 His Tag
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.: 183 / 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: 1.98 Å3/Da / Density % sol: 37.84 % / Description: Tringular shaped
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 100mM HEPES buffer, 1.4M Sodium citrate / PH range: 7.3-7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 14, 2013
RadiationMonochromator: Graphite Graphic crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.89→38 Å / Num. obs: 23438 / % possible obs: 100 % / Redundancy: 5.3 % / Biso Wilson estimate: 22.1 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.066 / Net I/av σ(I): 22.7 / Net I/σ(I): 28.3
Reflection shellResolution: 1.89→1.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2301 / CC1/2: 0.99 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HO1

4ho1


Resolution: 1.89→35.59 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.86
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1205 5.14 %5%
Rwork0.155 ---
obs0.1572 23435 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.89→35.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2279 0 0 183 2462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062329
X-RAY DIFFRACTIONf_angle_d0.8173173
X-RAY DIFFRACTIONf_dihedral_angle_d10.9651412
X-RAY DIFFRACTIONf_chiral_restr0.055381
X-RAY DIFFRACTIONf_plane_restr0.006408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8898-1.96550.28911340.22382423X-RAY DIFFRACTION99
1.9655-2.05490.19391260.16522466X-RAY DIFFRACTION100
2.0549-2.16320.20591450.14382440X-RAY DIFFRACTION100
2.1632-2.29870.22451220.16682485X-RAY DIFFRACTION100
2.2987-2.47620.22561330.14592437X-RAY DIFFRACTION100
2.4762-2.72530.20641500.15322445X-RAY DIFFRACTION100
2.7253-3.11940.17831500.14922473X-RAY DIFFRACTION100
3.1194-3.92940.19971240.14172500X-RAY DIFFRACTION100
3.9294-35.59650.17031210.15832561X-RAY DIFFRACTION100

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