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- PDB-6aif: Crystal structure of M120A mutant of O-acetylserine sulfhydrylase... -

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Basic information

Entry
Database: PDB / ID: 6aif
TitleCrystal structure of M120A mutant of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with high affinity inhibitory peptide from serine acetyl transferase of Salmonella typhimurium
Components
  • Cysteine synthase
  • Peptide from Serine acetyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / CysK M120 mutant / O-acetylserine sulfhydrylase / CysK/Peptide inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


serine O-acetyltransferase / serine O-acetyltransferase activity / cysteine synthase / L-cysteine desulfhydrase activity / cysteine synthase activity / cysteine biosynthetic process from serine / cytosol / cytoplasm
Similarity search - Function
Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / : / Serine acetyltransferase, N-terminal domain superfamily / Serine acetyltransferase, LbH domain / Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site ...Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / : / Serine acetyltransferase, N-terminal domain superfamily / Serine acetyltransferase, LbH domain / Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / : / Rossmann fold - #1100 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Trimeric LpxA-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Serine acetyltransferase / Cysteine synthase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
Salmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSingh, R.P. / Kaushik, A.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research India
CitationJournal: To Be Published
Title: Crystal structure of M120A mutant of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with high affinity inhibitory peptide from serine acetyl transferase of Salmonella typhimurium
Authors: Singh, R.P. / Kaushik, A.
History
DepositionAug 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)38,3702
Polymers38,3702
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-7 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.160, 112.160, 43.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 37144.273 Da / Num. of mol.: 1 / Mutation: M120A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: cysK, HI_1103 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P45040, cysteine synthase
#2: Protein/peptide Peptide from Serine acetyltransferase / SAT / Serine transacetylase


Mass: 1225.286 Da / Num. of mol.: 1 / Mutation: H1W / Source method: obtained synthetically
Source: (synth.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P29847
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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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: 1.78 Å3/Da / Density % sol: 30.94 %
Crystal growTemperature: 291.1 K / Method: vapor diffusion, sitting drop / pH: 7.7 / Details: 0.1M HEPES pH 7.7, 1.4M Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→35.47 Å / Num. obs: 12233 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 23.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.073 / Net I/σ(I): 25
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 9.4 / Num. unique obs: 1210 / CC1/2: 0.977 / Rrim(I) all: 0.255 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HO1

4ho1


Resolution: 2.3→35.468 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2136 568 4.64 %
Rwork0.1609 --
obs0.1635 12229 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→35.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 0 46 2393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082387
X-RAY DIFFRACTIONf_angle_d0.8713243
X-RAY DIFFRACTIONf_dihedral_angle_d12.4311442
X-RAY DIFFRACTIONf_chiral_restr0.055385
X-RAY DIFFRACTIONf_plane_restr0.005418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.53140.22981380.14962877X-RAY DIFFRACTION100
2.5314-2.89760.25591410.17282898X-RAY DIFFRACTION100
2.8976-3.65010.2331300.17022928X-RAY DIFFRACTION100
3.6501-35.47230.18511590.15372958X-RAY DIFFRACTION100

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