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- PDB-7yof: Crystal Structure of Triple mutant (D67E, A68P, I88L) of O-acetyl... -

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Basic information

Entry
Database: PDB / ID: 7yof
TitleCrystal Structure of Triple mutant (D67E, A68P, I88L) of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae at 2.3 A
ComponentsCysteine synthase
KeywordsTRANSFERASE / Triple mutant (D67E / A68P / I88L) / O-acetyl-L-serine sulfhydrylase / Haemophilus influenzae
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: 2.3 Å
AuthorsKumar, N. / Rahisuddin, R. / Saini, N. / Singh, A.K.
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 I88L single mutant of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae at 2.3 A
Authors: Kumar, N. / Rahisuddin, R. / Saini, N. / Singh, A.K.
History
DepositionAug 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release

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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)33,6921
Polymers33,6921
Non-polymers00
Water68538
1
A: Cysteine synthase

A: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)67,3832
Polymers67,3832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area4180 Å2
ΔGint-18 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.200, 112.200, 43.740
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 / O-acetyl-L-serine sulfhydrylase


Mass: 33691.527 Da / Num. of mol.: 1 / Mutation: D67E, A68P, I88L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae Rd KW20 (bacteria)
Gene: cysK, HI_1103 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P45040, cysteine synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES, 1.3M sodium citrate / PH range: 7.3-7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 27, 2014
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.3→40.75 Å / Num. obs: 235300 / % possible obs: 99.98 % / Redundancy: 19.1 % / CC1/2: 0.847 / CC star: 0.958 / Net I/σ(I): 66.54
Reflection shellResolution: 2.3→2.382 Å / Mean I/σ(I) obs: 13.29 / Num. unique obs: 1178 / CC1/2: 0.781 / CC star: 0.936

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y7L

1y7l


Resolution: 2.3→40.75 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.273 / SU ML: 0.151 / Cross valid method: FREE R-VALUE / ESU R: 0.406 / ESU R Free: 0.233
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.222 575 4.677 %
Rwork0.171 11719 -
all0.173 --
obs-12294 99.951 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.432 Å2
Baniso -1Baniso -2Baniso -3
1--2.135 Å20 Å20 Å2
2---2.135 Å20 Å2
3---4.27 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 0 38 2357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122355
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.6343193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7645309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.46822.34798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10615406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3211514
X-RAY DIFFRACTIONr_chiral_restr0.1070.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021722
X-RAY DIFFRACTIONr_nbd_refined0.2080.21076
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21631
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.293
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2440.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.211
X-RAY DIFFRACTIONr_mcbond_it2.7423.1631239
X-RAY DIFFRACTIONr_mcangle_it4.3384.7361547
X-RAY DIFFRACTIONr_scbond_it3.493.3341115
X-RAY DIFFRACTIONr_scangle_it5.1514.8341646
X-RAY DIFFRACTIONr_lrange_it8.05558.59810249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.265450.22835X-RAY DIFFRACTION100
2.36-2.4240.26350.205846X-RAY DIFFRACTION100
2.424-2.4950.25350.192817X-RAY DIFFRACTION100
2.495-2.5710.217490.204802X-RAY DIFFRACTION100
2.571-2.6550.265440.18747X-RAY DIFFRACTION100
2.655-2.7490.248310.185750X-RAY DIFFRACTION100
2.749-2.8520.177450.171699X-RAY DIFFRACTION100
2.852-2.9690.271270.159689X-RAY DIFFRACTION100
2.969-3.10.189270.165664X-RAY DIFFRACTION100
3.1-3.2510.199330.166645X-RAY DIFFRACTION100
3.251-3.4270.198410.161597X-RAY DIFFRACTION100
3.427-3.6340.256260.167587X-RAY DIFFRACTION100
3.634-3.8850.21260.16530X-RAY DIFFRACTION100
3.885-4.1950.259280.153499X-RAY DIFFRACTION100
4.195-4.5940.216260.155464X-RAY DIFFRACTION100
4.594-5.1340.154150.158433X-RAY DIFFRACTION100
5.134-5.9250.31120.178387X-RAY DIFFRACTION100
5.925-7.2460.207140.21320X-RAY DIFFRACTION100
7.246-10.2050.17970.136262X-RAY DIFFRACTION100
10.205-40.750.15290.135146X-RAY DIFFRACTION99.359

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