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- PDB-7yok: Crystal Structure of Tetra mutant (D67E, A68P, L98I, A301S) tetra... -

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Basic information

Entry
Database: PDB / ID: 7yok
TitleCrystal Structure of Tetra mutant (D67E, A68P, L98I, A301S) tetra mutant of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae at 2.8 A
ComponentsCysteine synthase
KeywordsTRANSFERASE / Tetra mutant (D67E / A68P / L98I / A301S) / 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: 2.799 Å
AuthorsSaini, N. / Kumar, N. / Rahisuddin, R. / 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 Tetra mutant (D67E, A68P, L98I, A301S) tetra mutant of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae at 2.8 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)33,7081
Polymers33,7081
Non-polymers00
Water25214
1
A: Cysteine synthase

A: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)67,4152
Polymers67,4152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area3800 Å2
ΔGint-19 kcal/mol
Surface area24060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.043, 113.043, 44.343
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: 33707.527 Da / Num. of mol.: 1 / Mutation: D67E, A68P, L98I, A301S
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.: 14 / 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: 2.14 Å3/Da / Density % sol: 42.7 %
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: Sep 11, 2012
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.8→39.97 Å / Num. obs: 6815 / % possible obs: 87.33 % / Redundancy: 1.1 % / CC1/2: 1 / CC star: 1 / Net I/σ(I): 31.05
Reflection shellResolution: 2.802→2.902 Å / Mean I/σ(I) obs: 12.88 / Num. unique obs: 505 / CC1/2: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y7L

1y7l


Resolution: 2.799→39.97 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.911 / SU B: 18.843 / SU ML: 0.371 / Cross valid method: FREE R-VALUE / ESU R Free: 0.493
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.265 294 4.747 %
Rwork0.2286 5900 -
all0.23 --
obs-6194 87.154 %
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: 75.712 Å2
Baniso -1Baniso -2Baniso -3
1--7.107 Å20 Å20 Å2
2---7.107 Å20 Å2
3---14.213 Å2
Refinement stepCycle: LAST / Resolution: 2.799→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 0 14 2300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122320
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.6343144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2425306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.68222.39696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89715402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0261514
X-RAY DIFFRACTIONr_chiral_restr0.1150.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021695
X-RAY DIFFRACTIONr_nbd_refined0.2190.21019
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21612
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.267
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3180.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2430.27
X-RAY DIFFRACTIONr_mcbond_it7.8017.5561227
X-RAY DIFFRACTIONr_mcangle_it11.92211.3071532
X-RAY DIFFRACTIONr_scbond_it9.0227.6251093
X-RAY DIFFRACTIONr_scangle_it13.12711.3021612
X-RAY DIFFRACTIONr_lrange_it19.185142.7859932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.799-2.8710.267120.201353X-RAY DIFFRACTION69.26
2.871-2.950.301150.24365X-RAY DIFFRACTION73.0769
2.95-3.0350.336230.302360X-RAY DIFFRACTION79.7917
3.035-3.1290.34290.283379X-RAY DIFFRACTION84.8233
3.129-3.2310.308320.276390X-RAY DIFFRACTION93.9866
3.231-3.3440.337110.254431X-RAY DIFFRACTION94.6467
3.344-3.470.366120.292379X-RAY DIFFRACTION90.3002
3.47-3.6120.268230.277354X-RAY DIFFRACTION91.7275
3.612-3.7720.321140.234313X-RAY DIFFRACTION80.9406
3.772-3.9550.174120.229321X-RAY DIFFRACTION88.8
3.955-4.1690.327100.204336X-RAY DIFFRACTION93.7669
4.169-4.4210.185180.183296X-RAY DIFFRACTION91.8129
4.421-4.7250.214110.196301X-RAY DIFFRACTION95.7055
4.725-5.1020.262160.198269X-RAY DIFFRACTION93.1373
5.102-5.5870.358110.22252X-RAY DIFFRACTION91.0035
5.587-6.2430.385130.246222X-RAY DIFFRACTION91.7969
6.243-7.2010.26780.248202X-RAY DIFFRACTION92.1053
7.201-8.8020.19260.192168X-RAY DIFFRACTION90.1554
8.802-12.3730.188130.186131X-RAY DIFFRACTION91.7197
12.373-39.970.27550.24878X-RAY DIFFRACTION88.2979

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