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- PDB-5dbe: Crystal structure of O-acetylserine sulfhydrylase from Haemophilu... -

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Basic information

Entry
Database: PDB / ID: 5dbe
TitleCrystal structure of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with pre-reactive O-acetyl serine, alpha-aminoacrylate reaction intermediate and peptide inhibitor at the resolution of 2.25A
Components
  • C-terminal peptide from Serine acetyltransferase
  • Cysteine synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / AMINO-ACID BIOSYNTHESIS / CYSTEINE BIOSYNTHESIS / TRANSFERASE / PYRIDOXAL PHOSPHATE / TRANSFERASE-TRANSFERASE INHIBITOR COMP / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


serine O-acetyltransferase / serine O-acetyltransferase activity / L-cysteine desulfhydrase activity / cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine / cytoplasm / cytosol
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
Chem-0JO / O-ACETYLSERINE / Serine acetyltransferase / Cysteine synthase
Similarity search - Component
Biological speciesHaemophilus influenzae KW20 (bacteria)
Salmonella typhimurium LT2 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSingh, A.K. / Kaushik, A. / Ekka, M.K. / Kumaran, S.
CitationJournal: To Be Published
Title: Crystal Structure Of O-Acetylserine Sulfhydrylase From Haemophilus Influenzae In Complex With Pre-Reactive O-Acetyl Serine, Alpha-Aminoacrylate Reactionintermediate And Peptide Inhibitor At The Resolution Of 2.25A
Authors: Singh, A.K. / Kaushik, A. / Ekka, M.K. / Kumaran, S.
History
DepositionAug 21, 2015Deposition site: RCSB / Processing site: PDBJ
SupersessionSep 9, 2015ID: 4ZU8
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Non-polymer description
Revision 1.2Nov 8, 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
X: Cysteine synthase
A: C-terminal peptide from Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0576
Polymers36,4102
Non-polymers6484
Water79344
1
X: Cysteine synthase
A: C-terminal peptide from Serine acetyltransferase
hetero molecules

X: Cysteine synthase
A: C-terminal peptide from Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,11412
Polymers72,8194
Non-polymers1,2958
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area6570 Å2
ΔGint-29 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.643, 112.643, 45.898
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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Protein / Protein/peptide , 2 types, 2 molecules XA

#1: Protein Cysteine synthase / CSase / O-acetylserine (thiol)-lyase / OAS-TL / O-acetylserine sulfhydrylase


Mass: 35232.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae KW20 (bacteria) / Strain: KW20 / Gene: cysK, HI_1103 / Plasmid: pET28A
Details (production host): kanamycin resisitant gene, iptg inducble, N erminal His tag
Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P45040, cysteine synthase
#2: Protein/peptide C-terminal peptide from Serine acetyltransferase / SAT / Serine transacetylase


Mass: 1177.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Salmonella typhimurium LT2 (bacteria) / References: UniProt: P29847

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Non-polymers , 4 types, 48 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-OAS / O-ACETYLSERINE


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Chemical ChemComp-0JO / 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid


Mass: 316.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N2O7P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 1.94 Å3/Da / Density % sol: 40 % / Description: TRIANGLE SHAPED
Crystal growTemperature: 293 K / Method: liquid diffusion
Details: 0.1M HEPES, 1.2M SODIUM CITRATE, VAPOR DIFFUSION, SITTING DROP
PH range: 7.4-7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 15, 2011 / Details: vaimax Hf optics
RadiationMonochromator: GRAPHITE POLAR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→35 Å / Num. obs: 13894 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 42.8
Reflection shellResolution: 2.25→2.35 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 8.6 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HO1

4ho1


Resolution: 2.25→35 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 692 4.98 %random selection
Rwork0.1825 ---
obs0.1848 13894 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2261 0 43 44 2348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082330
X-RAY DIFFRACTIONf_angle_d1.1743158
X-RAY DIFFRACTIONf_dihedral_angle_d15.218841
X-RAY DIFFRACTIONf_chiral_restr0.043376
X-RAY DIFFRACTIONf_plane_restr0.006406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.246-2.41940.28791390.2132603X-RAY DIFFRACTION99
2.4194-2.66280.25821470.19022598X-RAY DIFFRACTION100
2.6628-3.04790.22761300.18412660X-RAY DIFFRACTION100
3.0479-3.83940.24681300.18672631X-RAY DIFFRACTION99
3.8394-100.19981460.1722710X-RAY DIFFRACTION100

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