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- PDB-2efy: Crystal Structure of T.th. HB8 O-acetylserine sulfhydrylase Compl... -

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Basic information

Entry
Database: PDB / ID: 2efy
TitleCrystal Structure of T.th. HB8 O-acetylserine sulfhydrylase Complexed with 4-Acetylbutyric acid
ComponentsO-acetylserine (Thiol)-lyase
KeywordsTRANSFERASE / PLP-dependent enzyme
Function / homology
Function and homology information


cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine
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. / : / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold ...Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-OXOHEXANOIC ACID / PYRIDOXAL-5'-PHOSPHATE / Cysteine synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsGoto, M.
CitationJournal: to be published
Title: Crystal Structure of T.th. HB8 O-acetylserine sulfhydrylase Complexed with 4-Acetylbutyric acid
Authors: Goto, M.
History
DepositionFeb 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-acetylserine (Thiol)-lyase
B: O-acetylserine (Thiol)-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8856
Polymers66,1302
Non-polymers7554
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-15 kcal/mol
Surface area21560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.760, 100.760, 65.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein O-acetylserine (Thiol)-lyase / O-acetylserine sulfhydrylase / Cysteine synthase


Mass: 33065.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RP / References: UniProt: Q5SLE6, cysteine synthase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-4AT / 5-OXOHEXANOIC ACID / 4-ACETYLBUTYRIC ACID


Mass: 130.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: tri-sodium citrate, CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 27420 / Num. obs: 26941 / % possible obs: 98.2 % / Biso Wilson estimate: 26.5 Å2
Reflection shellResolution: 2.35→2.43 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VE1

1ve1


Resolution: 2.35→48.11 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1773193.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2683 10 %RANDOM
Rwork0.193 ---
obs0.193 26941 98.1 %-
all-27420 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.5266 Å2 / ksol: 0.333373 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2--0.51 Å20 Å2
3----1.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.35→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4532 0 48 161 4741
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scbond_it23.222
X-RAY DIFFRACTIONc_scangle_it21.172.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 462 10.2 %
Rwork0.237 4052 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwat.top
X-RAY DIFFRACTION34ab.param4ab.top
X-RAY DIFFRACTION4plp.paramplp.top
X-RAY DIFFRACTION5etc.paramintshiff.top

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