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- PDB-7yoe: Crystal Structure of A68P single mutant of O-acetyl-L-serine sulf... -

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Basic information

Entry
Database: PDB / ID: 7yoe
TitleCrystal Structure of A68P single mutant of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae at 1.88 A
ComponentsCysteine synthase
KeywordsTRANSFERASE / A68P single mutant / O-acetyl-L-serine sulfhydrylase / Haemophilus influenzae
Function / homology
Function and homology information


cysteine synthase / L-cysteine desulfhydrase activity / 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 / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme
Similarity search - Domain/homology
Biological speciesHaemophilus influenzae Rd KW20 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.88 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 A68P single mutant of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae at 1.88 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)33,6781
Polymers33,6781
Non-polymers00
Water82946
1
A: Cysteine synthase

A: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)67,3552
Polymers67,3552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area4320 Å2
ΔGint-19 kcal/mol
Surface area22730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.281, 112.281, 43.744
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: 33677.504 Da / Num. of mol.: 1 / Mutation: A68P
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 / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.08 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.1M HEPES, 1.3M Sodium citrate / PH range: 7.3-7.9

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Data collection

DiffractionMean temperature: 293 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: Jun 24, 2012
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.88→39.7 Å / Num. obs: 22383 / % possible obs: 99.64 % / Redundancy: 1.1 % / CC1/2: 1 / Net I/σ(I): 14.75
Reflection shellResolution: 1.88→1.947 Å / Mean I/σ(I) obs: 2.01 / Num. unique obs: 2171 / CC1/2: 1 / % possible all: 97.48

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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: 1.88→39.7 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.416 / SU ML: 0.124 / Cross valid method: FREE R-VALUE / ESU R: 0.172 / ESU R Free: 0.141
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2215 1044 4.664 %
Rwork0.2014 21339 -
all0.202 --
obs-22383 99.546 %
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: 34.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.922 Å20 Å2-0 Å2
2---1.922 Å2-0 Å2
3---3.845 Å2
Refinement stepCycle: LAST / Resolution: 1.88→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2326 0 0 46 2372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122362
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.6343202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7855310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.29522.34798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94515408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2971514
X-RAY DIFFRACTIONr_chiral_restr0.1130.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021726
X-RAY DIFFRACTIONr_nbd_refined0.2120.21094
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21653
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2105
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2090.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.213
X-RAY DIFFRACTIONr_mcbond_it3.0853.3631243
X-RAY DIFFRACTIONr_mcangle_it4.5195.0251552
X-RAY DIFFRACTIONr_scbond_it3.7543.5811119
X-RAY DIFFRACTIONr_scangle_it5.2335.2041650
X-RAY DIFFRACTIONr_lrange_it7.54763.23610318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.9270.367670.2931490X-RAY DIFFRACTION95.5215
1.927-1.980.318680.2591541X-RAY DIFFRACTION99.0154
1.98-2.0370.289930.2511440X-RAY DIFFRACTION99.7398
2.037-2.10.231620.2231471X-RAY DIFFRACTION100
2.1-2.1680.238780.2211390X-RAY DIFFRACTION100
2.168-2.2440.214550.211369X-RAY DIFFRACTION100
2.244-2.3290.261560.2091323X-RAY DIFFRACTION100
2.329-2.4240.253550.2011284X-RAY DIFFRACTION100
2.424-2.5320.283530.2071201X-RAY DIFFRACTION100
2.532-2.6550.197490.2081189X-RAY DIFFRACTION100
2.655-2.7990.254710.2041078X-RAY DIFFRACTION100
2.799-2.9680.247510.1991050X-RAY DIFFRACTION100
2.968-3.1730.185490.185992X-RAY DIFFRACTION100
3.173-3.4270.234390.197932X-RAY DIFFRACTION100
3.427-3.7530.192600.187826X-RAY DIFFRACTION100
3.753-4.1950.183250.137781X-RAY DIFFRACTION99.6292
4.195-4.8420.168310.166701X-RAY DIFFRACTION99.8636
4.842-5.9240.214300.193576X-RAY DIFFRACTION100
5.924-8.3550.242430.201432X-RAY DIFFRACTION100
8.355-39.70.13890.168273X-RAY DIFFRACTION98.2578

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