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- PDB-2cb1: Crystal Structure of O-actetyl Homoserine Sulfhydrylase From Ther... -

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Basic information

Entry
Database: PDB / ID: 2cb1
TitleCrystal Structure of O-actetyl Homoserine Sulfhydrylase From Thermus Thermophilus HB8,OAH2.
ComponentsO-ACETYL HOMOSERINE SULFHYDRYLASE
KeywordsLYASE / PLP ENZYME / SULFHYDRYLASE / HOMOSERINE / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / STRUCTURAL GENOMICS
Function / homology
Function and homology information


O-acetylhomoserine sulfhydrylase activity / L-homocysteine biosynthetic process / cysteine synthase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / transsulfuration / cysteine biosynthetic process from serine / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
O-acetylhomoserine/O-acetylserine sulfhydrylase / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...O-acetylhomoserine/O-acetylserine sulfhydrylase / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / O-acetyl-L-homoserine sulfhydrylase 2 / O-acetyl-L-homoserine sulfhydrylase 2
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsImagawa, T. / Utsunomiya, H. / Tsuge, H. / Ebihara, A. / Kanagawa, M. / Nakagawa, N. / Kuroishi, C. / Agari, Y. / Kuramitsu, S. / Yokoyama, S.
CitationJournal: To be Published
Title: The Crystal Structure of O-Acetyl Homoserine Sulfhydrylase
Authors: Imagawa, T. / Utsunomiya, H. / Agari, Y. / Satoh, S. / Tsuge, H.
History
DepositionDec 28, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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-ACETYL HOMOSERINE SULFHYDRYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4792
Polymers44,2321
Non-polymers2471
Water2,648147
1
A: O-ACETYL HOMOSERINE SULFHYDRYLASE
hetero molecules

A: O-ACETYL HOMOSERINE SULFHYDRYLASE
hetero molecules

A: O-ACETYL HOMOSERINE SULFHYDRYLASE
hetero molecules

A: O-ACETYL HOMOSERINE SULFHYDRYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,9168
Polymers176,9274
Non-polymers9894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation2_655-x+1,-y,z1
Buried area21400 Å2
ΔGint-141.4 kcal/mol
Surface area47840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.986, 86.392, 156.138
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein O-ACETYL HOMOSERINE SULFHYDRYLASE / O-ACETYL-L-HOMOSERINE SULFHYDRYLASE


Mass: 44231.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS HB8 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q76K51, UniProt: Q5SJ58*PLUS, EC: 4.2.99.10
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.13 Å3/Da / Density % sol: 42.37 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1
DetectorType: RIGAKU CCD / Detector: CCD / Date: May 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 25853 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 33.95
Reflection shellHighest resolution: 1.9 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 5.04 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E5F

1e5f


Resolution: 2→78.09 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.019 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1314 5.1 %RANDOM
Rwork0.187 ---
obs0.19 24539 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2--1.65 Å20 Å2
3----2.22 Å2
Refinement stepCycle: LAST / Resolution: 2→78.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3059 0 15 147 3221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0223136
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0281.9934269
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7565402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24622.698126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.31715498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2061528
X-RAY DIFFRACTIONr_chiral_restr0.1480.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022364
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.21484
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22136
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2171
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.296
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4291.52082
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.02323185
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.53131232
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3074.51084
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 84 -
Rwork0.201 1690 -
obs--93.52 %

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