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- PDB-7yom: Crystal structure of tetra mutant (D67E,A68P,L98I,A301S) of O-ace... -

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Basic information

Entry
Database: PDB / ID: 7yom
TitleCrystal structure of tetra mutant (D67E,A68P,L98I,A301S) of O-acetylserine sulfhydrylase from Salmonella typhimurium in complex with high-affinity inhibitory peptide from serine acetyltransferase of Salmonella typhimurium at 2.8 A
Components
  • Cysteine synthase
  • peptide from serine acetyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / tetra mutant (D67E / A68P / L98I / A301S) / O-acetylserine sulfhydrylase / Salmonella typhimurium / high-affinity inhibitory peptide from serine acetyltransferase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


cysteine synthase / cystathionine beta-synthase activity / cysteine synthase activity / L-cysteine desulfhydrase 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)
Salmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 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 I88L single mutant of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with high-affinity inhibitory peptide from serine acetyltransferase of Salmonella ...Title: Crystal structure of I88L single mutant of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with high-affinity inhibitory peptide from serine acetyltransferase of Salmonella typhimurium at 2.14 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
B: peptide from serine acetyltransferase


Theoretical massNumber of molelcules
Total (without water)34,6082
Polymers34,6082
Non-polymers00
Water1267
1
A: Cysteine synthase
B: peptide from serine acetyltransferase

A: Cysteine synthase
B: peptide from serine acetyltransferase


Theoretical massNumber of molelcules
Total (without water)69,2174
Polymers69,2174
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area5550 Å2
ΔGint-34 kcal/mol
Surface area23050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.140, 113.140, 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: 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: Protein/peptide peptide from serine acetyltransferase /


Mass: 900.930 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Salmonella typhimurium (bacteria)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.12 Å3/Da / Density % sol: 42.03 %
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: May 8, 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→40.831 Å / Num. obs: 69653 / % possible obs: 97.66 % / Redundancy: 10.1 % / Biso Wilson estimate: 24.22 Å2 / CC1/2: 0.713 / Rmerge(I) obs: 0.6911 / Net I/σ(I): 42.47
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 691 / CC1/2: 0.634 / CC star: 0.881 / % possible all: 100

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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: 2.8→40.831 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.835 / SU B: 16.951 / SU ML: 0.339 / Cross valid method: FREE R-VALUE / ESU R Free: 0.467
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2723 349 5.105 %
Rwork0.2156 6488 -
all0.218 --
obs-6837 97.657 %
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: 22.582 Å2
Baniso -1Baniso -2Baniso -3
1--0.508 Å20 Å20 Å2
2---0.508 Å20 Å2
3---1.016 Å2
Refinement stepCycle: LAST / Resolution: 2.8→40.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2303 0 0 7 2310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122337
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.6333166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6125308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05422.63295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.9215402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.421513
X-RAY DIFFRACTIONr_chiral_restr0.1080.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021705
X-RAY DIFFRACTIONr_nbd_refined0.2160.21041
X-RAY DIFFRACTIONr_nbtor_refined0.30.21596
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.269
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2440.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2390.26
X-RAY DIFFRACTIONr_mcbond_it1.6592.181238
X-RAY DIFFRACTIONr_mcangle_it2.6913.2651544
X-RAY DIFFRACTIONr_scbond_it2.3632.3431099
X-RAY DIFFRACTIONr_scangle_it3.4223.4151622
X-RAY DIFFRACTIONr_lrange_it6.06141.0919980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.8730.259290.232501X-RAY DIFFRACTION100
2.873-2.9520.391270.214460X-RAY DIFFRACTION100
2.952-3.0370.284290.236445X-RAY DIFFRACTION100
3.037-3.130.35260.212454X-RAY DIFFRACTION100
3.13-3.2330.281280.22421X-RAY DIFFRACTION100
3.233-3.3460.289200.199429X-RAY DIFFRACTION100
3.346-3.4720.349160.191408X-RAY DIFFRACTION99.7647
3.472-3.6140.233260.233379X-RAY DIFFRACTION97.5904
3.614-3.7740.403140.326359X-RAY DIFFRACTION96.3824
3.774-3.9580.295210.245366X-RAY DIFFRACTION99.2308
3.958-4.1710.185160.185331X-RAY DIFFRACTION99.4269
4.171-4.4240.218200.181316X-RAY DIFFRACTION99.115
4.424-4.7280.225140.171301X-RAY DIFFRACTION96.9231
4.728-5.1060.212180.169276X-RAY DIFFRACTION97.0297
5.106-5.5910.29590.203262X-RAY DIFFRACTION95.7597
5.591-6.2470.421150.222225X-RAY DIFFRACTION96
6.247-7.2060.31560.207201X-RAY DIFFRACTION91.5929
7.206-8.8070.21340.165169X-RAY DIFFRACTION90.1042
8.807-9.010.11911120X-RAY DIFFRACTION85.0649
12.38-40.83100.25965X-RAY DIFFRACTION69.8925

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