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- PDB-8gsk: Crystal Structure of S302G single mutant of O-acetyl-L-serine sul... -

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Basic information

Entry
Database: PDB / ID: 8gsk
TitleCrystal Structure of S302G single mutant of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae at 2.2 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 / L-cysteine biosynthetic process from L-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: 2.271 Å
AuthorsKumar, N. / Mahajan, A.S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR5236/MED/29/504/20 India
CitationJournal: To Be Published
Title: S302G Crystal Structure of S302G single mutant of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae at 2.2 A
Authors: Kumar, N. / Mahajan, A.S.
History
DepositionSep 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)33,6211
Polymers33,6211
Non-polymers00
Water905
1
A: Cysteine synthase

A: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)67,2432
Polymers67,2432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area4020 Å2
ΔGint-19 kcal/mol
Surface area23360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.600, 112.600, 45.730
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


Mass: 33621.438 Da / Num. of mol.: 1 / Mutation: S302G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae Rd KW20 (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / 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.: 5 / 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: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 1.3 M Sodium Citrate

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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 4, 2014
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.271→42.37 Å / Num. obs: 12952 / % possible obs: 96.02 % / Redundancy: 14.4 % / CC1/2: 0.788 / CC star: 0.939 / Net I/σ(I): 44.88
Reflection shellResolution: 2.271→2.352 Å / Num. unique obs: 18871 / CC1/2: 0.745

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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: 2.271→42.37 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.897 / SU B: 9.415 / SU ML: 0.223 / Cross valid method: FREE R-VALUE / ESU R: 0.44 / ESU R Free: 0.268
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2664 625 4.839 %
Rwork0.2225 12291 -
all0.225 --
obs-12916 96.023 %
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: 32.709 Å2
Baniso -1Baniso -2Baniso -3
1--2.295 Å2-0 Å20 Å2
2---2.295 Å2-0 Å2
3---4.59 Å2
Refinement stepCycle: LAST / Resolution: 2.271→42.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 0 5 2275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122303
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.6313128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0265308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99122.6694
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.44115381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3851513
X-RAY DIFFRACTIONr_chiral_restr0.1190.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021694
X-RAY DIFFRACTIONr_nbd_refined0.2290.21046
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21581
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.285
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2040.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.190.210
X-RAY DIFFRACTIONr_mcbond_it2.23.2641235
X-RAY DIFFRACTIONr_mcangle_it3.3924.8821542
X-RAY DIFFRACTIONr_scbond_it2.5363.361068
X-RAY DIFFRACTIONr_scangle_it3.7014.9561586
X-RAY DIFFRACTIONr_lrange_it5.93960.8119709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.271-2.330.475360.391924X-RAY DIFFRACTION96.7742
2.33-2.3930.301540.301903X-RAY DIFFRACTION100
2.393-2.4630.411340.256877X-RAY DIFFRACTION99.8904
2.463-2.5380.334440.226873X-RAY DIFFRACTION100
2.538-2.6220.239500.223823X-RAY DIFFRACTION100
2.622-2.7140.357280.238619X-RAY DIFFRACTION75.5841
2.714-2.8160.326300.221788X-RAY DIFFRACTION100
2.816-2.9310.295440.233751X-RAY DIFFRACTION99.8744
2.931-3.0610.308410.21731X-RAY DIFFRACTION100
3.061-3.210.28440.206680X-RAY DIFFRACTION100
3.21-3.3830.255320.213662X-RAY DIFFRACTION100
3.383-3.5880.259340.223495X-RAY DIFFRACTION80.0303
3.588-3.8350.237290.258498X-RAY DIFFRACTION85.1373
3.835-4.1420.239320.213483X-RAY DIFFRACTION88.6403
4.142-4.5360.232140.187519X-RAY DIFFRACTION100
4.536-5.0690.144240.181455X-RAY DIFFRACTION100
5.069-5.8490.28200.203417X-RAY DIFFRACTION100
5.849-7.1540.199130.222352X-RAY DIFFRACTION100
7.154-10.0770.176100.187280X-RAY DIFFRACTION100
10.077-42.370.326120.183161X-RAY DIFFRACTION99.4253

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