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- PDB-7c35: Crystal structure of M96A mutant of O-acetyl-L-serine sulfhydryla... -

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Basic information

Entry
Database: PDB / ID: 7c35
TitleCrystal structure of M96A mutant of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae
ComponentsCysteine synthase
KeywordsTRANSFERASE / PLP dependent enzyme / Cysteine metabolizing Enzyme / O acetyl transferase enzyme
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. / : / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme
Similarity search - Domain/homology
Biological speciesHaemophilus influenzae Rd KW20 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAbhishek, K. / Rahisuddin, R. / Kumaran, S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR5236/MED/29/504/2012 India
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Molecular mechanism of selective substrate engagement and inhibitor disengagement of cysteine synthase.
Authors: Kaushik, A. / Rahisuddin, R. / Saini, N. / Singh, R.P. / Kaur, R. / Koul, S. / Kumaran, S.
History
DepositionMay 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: 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 1.2Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
A: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)37,1441
Polymers37,1441
Non-polymers00
Water1,76598
1
A: Cysteine synthase

A: 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_775-x+2,-y+2,z1
Buried area3850 Å2
ΔGint-20 kcal/mol
Surface area21960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.010, 113.010, 44.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: M96A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae Rd KW20 (bacteria)
Gene: cysK, HI_1103 / Plasmid: pET28a+
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.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.89 Å3/Da / Density % sol: 35.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 100mM Hepes buffer pH 7.4, 1.4M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 2013
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→35.762 Å / Num. obs: 16477 / % possible obs: 99.52 % / Redundancy: 3.9 % / Biso Wilson estimate: 32.28 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.087 / Net I/σ(I): 10.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.01 / Num. unique obs: 2379 / CC1/2: 0.866 / CC star: 0.963 / Rrim(I) all: 0.315 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HO1

4ho1


Resolution: 2.1→35.74 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 831 5.06 %
Rwork0.1766 15603 -
obs0.1787 16434 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.18 Å2 / Biso mean: 37.7276 Å2 / Biso min: 18.43 Å2
Refinement stepCycle: final / Resolution: 2.1→35.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2241 0 0 98 2339
Biso mean---37.44 -
Num. residues----307
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.210.27051540.20092577100
2.23-2.40.27581430.2322253399
2.4-2.650.241450.18222590100
2.65-3.030.23111210.17572604100
3.03-3.810.21421430.16982602100
3.82-35.70.18691250.16212697100

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