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- PDB-7yod: Crystal structure of A68P single mutant of O-acetylserine sulfhyd... -

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Basic information

Entry
Database: PDB / ID: 7yod
TitleCrystal structure of A68P single mutant of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with high-affinity inhibitory peptide from serine acetyltransferase of Salmonella typhimurium at 2.1 A
Components
  • Cysteine synthase
  • peptide from serine acetyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / A68P single mutant / O-acetyl-L-serine sulfhydrylase / Haemophilus influenzae / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
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)
Salmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.101 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-acetylserine sulfhydrylase from Haemophilus influenzae in complex with high-affinity inhibitory peptide from serine acetyltransferase of Salmonella typhimurium at 2.1 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)34,5782
Polymers34,5782
Non-polymers00
Water66737
1
A: Cysteine synthase
B: peptide from serine acetyltransferase

A: Cysteine synthase
B: peptide from serine acetyltransferase


Theoretical massNumber of molelcules
Total (without water)69,1574
Polymers69,1574
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area5650 Å2
ΔGint-39 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.599, 112.599, 45.822
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: 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


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.2 Å3/Da / Density % sol: 44.14 %
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: May 26, 2012
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.101→39.81 Å / Num. obs: 16969 / % possible obs: 99.95 % / Redundancy: 1.1 % / Biso Wilson estimate: 32.49 Å2 / CC1/2: 1 / Net I/σ(I): 37.22
Reflection shellResolution: 2.101→2.176 Å / Num. unique obs: 1671 / 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: 2.101→39.81 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.889 / SU B: 5.578 / SU ML: 0.153 / Cross valid method: FREE R-VALUE / ESU R: 0.279 / ESU R Free: 0.208
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2553 824 4.856 %
Rwork0.222 16143 -
all0.224 --
obs-16967 99.959 %
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: 37.309 Å2
Baniso -1Baniso -2Baniso -3
1--2.031 Å2-0 Å20 Å2
2---2.031 Å20 Å2
3---4.062 Å2
Refinement stepCycle: LAST / Resolution: 2.101→39.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2307 0 0 37 2344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122341
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.6333171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3225308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.14622.78497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13115403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5431513
X-RAY DIFFRACTIONr_chiral_restr0.1110.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021713
X-RAY DIFFRACTIONr_nbd_refined0.2180.21134
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21633
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.294
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.27
X-RAY DIFFRACTIONr_mcbond_it3.0013.5781238
X-RAY DIFFRACTIONr_mcangle_it4.0395.3491544
X-RAY DIFFRACTIONr_scbond_it3.7143.8741102
X-RAY DIFFRACTIONr_scangle_it5.1745.6481627
X-RAY DIFFRACTIONr_lrange_it7.64967.82810190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.101-2.1550.335410.2181182X-RAY DIFFRACTION99.674
2.155-2.2140.31750.211141X-RAY DIFFRACTION100
2.214-2.2780.315630.2061114X-RAY DIFFRACTION100
2.278-2.3480.25500.2121107X-RAY DIFFRACTION100
2.348-2.4250.31440.2271070X-RAY DIFFRACTION100
2.425-2.510.233690.2251011X-RAY DIFFRACTION100
2.51-2.6050.25560.221961X-RAY DIFFRACTION100
2.605-2.7110.296440.219961X-RAY DIFFRACTION100
2.711-2.8320.255430.228923X-RAY DIFFRACTION100
2.832-2.970.231370.243897X-RAY DIFFRACTION100
2.97-3.130.269520.245808X-RAY DIFFRACTION100
3.13-3.320.187480.218800X-RAY DIFFRACTION100
3.32-3.5480.32370.212732X-RAY DIFFRACTION100
3.548-3.8320.2260.223707X-RAY DIFFRACTION100
3.832-4.1970.219360.223645X-RAY DIFFRACTION100
4.197-4.6910.276290.203576X-RAY DIFFRACTION100
4.691-5.4130.258290.22511X-RAY DIFFRACTION100
5.413-6.6220.304190.248452X-RAY DIFFRACTION100
6.622-9.3330.215160.215349X-RAY DIFFRACTION100
9.333-39.810.234100.232198X-RAY DIFFRACTION98.5782

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