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- PDB-7yog: Crystal Structure of I88L single mutant of O-acetyl-L-serine sulf... -

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Basic information

Entry
Database: PDB / ID: 7yog
TitleCrystal Structure of I88L single mutant of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae at 2.3 A
ComponentsCysteine synthase
KeywordsTRANSFERASE / single mutant / 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)33,6511
Polymers33,6511
Non-polymers00
Water39622
1
A: Cysteine synthase

A: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)67,3032
Polymers67,3032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area4060 Å2
ΔGint-20 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.230, 112.230, 43.520
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: 33651.465 Da / Num. of mol.: 1 / Mutation: 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.: 22 / 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: 2.07 Å3/Da / Density % sol: 40.7 %
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: Aug 24, 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→40.609 Å / Num. obs: 12260 / % possible obs: 99.95 % / Redundancy: 18.5 % / Biso Wilson estimate: 34.52 Å2 / CC1/2: 0.912 / CC star: 0.977 / Net I/σ(I): 72.04
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 1212 / CC1/2: 0.76 / % possible all: 100

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Processing

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

1y7l


Resolution: 2.3→40.609 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.906 / SU B: 9.838 / SU ML: 0.234 / Cross valid method: FREE R-VALUE / σ(F): 1 / ESU R: 0.509 / ESU R Free: 0.281
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2682 613 5.001 %
Rwork0.2156 11645 -
all0.218 --
obs-12258 99.967 %
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: 43.602 Å2
Baniso -1Baniso -2Baniso -3
1--2.296 Å20 Å20 Å2
2---2.296 Å20 Å2
3---4.592 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 0 22 2338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122351
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.6333187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9715309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.6922.34798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.06415405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2891514
X-RAY DIFFRACTIONr_chiral_restr0.1110.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021718
X-RAY DIFFRACTIONr_nbd_refined0.2140.21065
X-RAY DIFFRACTIONr_nbtor_refined0.310.21631
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.289
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2410.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.190.27
X-RAY DIFFRACTIONr_mcbond_it3.9164.2181239
X-RAY DIFFRACTIONr_mcangle_it5.5866.3141547
X-RAY DIFFRACTIONr_scbond_it4.7744.4831111
X-RAY DIFFRACTIONr_scangle_it6.6886.521640
X-RAY DIFFRACTIONr_lrange_it9.33579.34510162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.365470.309843X-RAY DIFFRACTION100
2.36-2.4240.329470.271850X-RAY DIFFRACTION100
2.424-2.4950.213450.225794X-RAY DIFFRACTION100
2.495-2.5710.351420.237798X-RAY DIFFRACTION100
2.571-2.6560.295430.214737X-RAY DIFFRACTION100
2.656-2.7490.276460.205736X-RAY DIFFRACTION100
2.749-2.8520.213320.194726X-RAY DIFFRACTION100
2.852-2.9690.179310.189671X-RAY DIFFRACTION100
2.969-3.10.271320.181669X-RAY DIFFRACTION100
3.1-3.2520.266270.18630X-RAY DIFFRACTION100
3.252-3.4270.241260.23614X-RAY DIFFRACTION100
3.427-3.6350.356330.259584X-RAY DIFFRACTION100
3.635-3.8850.372370.341511X-RAY DIFFRACTION99.8178
3.885-4.1950.178220.209504X-RAY DIFFRACTION99.8102
4.195-4.5950.208220.164456X-RAY DIFFRACTION100
4.595-5.1350.176250.166425X-RAY DIFFRACTION100
5.135-5.9250.332170.19380X-RAY DIFFRACTION100
5.925-7.2460.289170.225316X-RAY DIFFRACTION100
7.246-10.2050.155130.147255X-RAY DIFFRACTION100
10.205-40.6090.25490.158146X-RAY DIFFRACTION98.7261

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