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- PDB-4nu8: Crystal structure of O-acetylserine sulfhydrylase from Haemophilu... -

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Basic information

Entry
Database: PDB / ID: 4nu8
TitleCrystal structure of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with high affinity inhibitory peptide from serine acetyl transferase of Salmonella typhimurium at 2.0 A
Components
  • Cysteine synthase
  • Peptide from Serine acetyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / alpha/beta fold / Rossmann fold CysK / catalytic activity cysteine synthase / transferase / serine acetyl 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 acetyltransferase, LbH domain / Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal domain superfamily / Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. ...Serine acetyltransferase, LbH domain / Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal domain superfamily / 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 / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Trimeric LpxA-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Serine acetyltransferase / Cysteine synthase / Serine acetyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
Salmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsEkka, M.K. / Kaushik, A. / Singh, A.K. / Kumaran, S.
CitationJournal: To be Published
Title: Crystal structure of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with high affinity inhibitory peptide from serine acetyl transferase of Salmonella Typhimurium at 2.0 A
Authors: Ekka, M.K. / Kaushik, A. / Singh, A.K. / Kumaran, S.
History
DepositionDec 3, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 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
X: Cysteine synthase
A: Peptide from Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4733
Polymers35,3812
Non-polymers921
Water1,45981
1
X: Cysteine synthase
A: Peptide from Serine acetyltransferase
hetero molecules

X: Cysteine synthase
A: Peptide from Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9476
Polymers70,7634
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area6730 Å2
ΔGint-32 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.322, 112.322, 45.800
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: 34480.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: IPTG inducible / Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: ATCC51907 / Gene: cysK, HI_1103 / Plasmid: pET 28A / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / 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 enterica (bacteria) / References: UniProt: Q8Z2E9, UniProt: P29847*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.4M sodium Citrate, 0.1M HEPES pH 7.5 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: Aug 12, 2012
RadiationMonochromator: Graphite polar / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→35.618 Å / Num. all: 17594 / Num. obs: 17594 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 31.97 Å2 / Net I/σ(I): 54.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HO1

4ho1


Resolution: 2.07→35.519 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8302 / SU ML: 0.27 / Isotropic thermal model: Isotropic Model / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2355 891 5.06 %RANDOM
Rwork0.1866 ---
all0.189 17610 --
obs0.189 17594 99.77 %-
Solvent computationShrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.275 Å2 / ksol: 0.412 e/Å3
Displacement parametersBiso max: 87.63 Å2 / Biso mean: 31.7 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--7.1113 Å2-0 Å20 Å2
2---7.1113 Å2-0 Å2
3---14.2226 Å2
Refinement stepCycle: LAST / Resolution: 2.07→35.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 6 81 2414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072385
X-RAY DIFFRACTIONf_angle_d1.0483242
X-RAY DIFFRACTIONf_dihedral_angle_d13.272859
X-RAY DIFFRACTIONf_chiral_restr0.069385
X-RAY DIFFRACTIONf_plane_restr0.005419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.0698-2.19950.24911530.17762745
2.1995-2.36920.2921380.20332771
2.3692-2.60760.2591420.1962777
2.6076-2.98480.25741530.18272777
2.9848-3.75980.21491680.17392772
3.7598-35.52450.22051370.19112861

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