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- PDB-7ewo: Crystal Structure of D67A, E68P double mutant of O-acetyl-L-serin... -

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Entry
Database: PDB / ID: 7ewo
TitleCrystal Structure of D67A, E68P double mutant of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae
ComponentsCysteine synthase
KeywordsTRANSFERASE / Evolution / Cysteine Synthase / Protein-Protein interaction
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. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme
Similarity search - Domain/homology
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRahisuddin, R. / Ekka, M.K. / Singh, A.K. / Saini, N. / Patel, M. / Kumar, N. / Kumaran, S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR5236/MED/29/504/2012 India
CitationJournal: To Be Published
Title: Crystal Structure of D67A, E68P double mutant of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae
Authors: Rahisuddin, R. / Ekka, M.K. / Singh, A.K. / Saini, N. / Patel, M. / Kumaran, S.
History
DepositionMay 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
A: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)37,2441
Polymers37,2441
Non-polymers00
Water52229
1
A: Cysteine synthase

A: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)74,4892
Polymers74,4892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area2630 Å2
ΔGint-20 kcal/mol
Surface area22670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.212, 113.212, 43.475
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 37244.453 Da / Num. of mol.: 1 / Mutation: D67E, A68P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (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 / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.87 Å3/Da / Density % sol: 34.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES, 1.3M 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: 1.5414 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 26, 2012
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5414 Å / Relative weight: 1
ReflectionResolution: 2.397→40.59 Å / Num. obs: 10586 / % possible obs: 95.93 % / Redundancy: 5.6 % / Biso Wilson estimate: 43.7 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 31.8
Reflection shellResolution: 2.397→2.483 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 786 / % possible all: 73.94

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HO1

4ho1


Resolution: 2.4→40.59 Å / SU ML: 0.2549 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.0497 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2566 502 4.74 %
Rwork0.1917 10082 -
obs0.1947 10584 95.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.68 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 0 28 2150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712153
X-RAY DIFFRACTIONf_angle_d0.9052937
X-RAY DIFFRACTIONf_chiral_restr0.0555358
X-RAY DIFFRACTIONf_plane_restr0.0065380
X-RAY DIFFRACTIONf_dihedral_angle_d14.08451292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.640.28731100.22282182X-RAY DIFFRACTION84.02
2.64-3.020.31391340.21962590X-RAY DIFFRACTION99.71
3.02-3.80.26011360.19572610X-RAY DIFFRACTION99.96
3.8-40.590.22971220.17642700X-RAY DIFFRACTION99.96
Refinement TLS params.Method: refined / Origin x: 15.0865181773 Å / Origin y: 3.72909906416 Å / Origin z: -4.49140423341 Å
111213212223313233
T0.300515033952 Å20.0314518798075 Å2-0.00314216072132 Å2-0.342497044388 Å20.00912037304842 Å2--0.319997372937 Å2
L1.79509115603 °20.301964823574 °20.0216965273698 °2-2.2531158712 °20.275575884911 °2--1.11700019552 °2
S0.034227002513 Å °-0.115505100984 Å °-0.277779711992 Å °0.155078122264 Å °0.0551789699883 Å °-0.00917516663743 Å °0.050379957225 Å °0.126462466358 Å °-0.092346023885 Å °
Refinement TLS groupSelection details: all

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