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- PDB-2ctz: Crystal structure of o-acetyl homoserine sulfhydrylase from Therm... -

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Basic information

Entry
Database: PDB / ID: 2ctz
TitleCrystal structure of o-acetyl homoserine sulfhydrylase from Thermus thermophilus HB8
ComponentsO-acetyl-L-homoserine sulfhydrylase
KeywordsTRANSFERASE / Crystal / o-acetyl homoserine sulfhydrase / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


O-acetylhomoserine sulfhydrylase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / transferase activity, transferring alkyl or aryl (other than methyl) groups / transsulfuration / methionine biosynthetic process / pyridoxal phosphate binding
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 1 / O-acetyl-L-homoserine sulfhydrylase 1
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsImagawa, T. / Kousumi, Y. / Tsuge, H. / Utsunomiya, H. / Ebihara, A. / Nakagawa, N. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of o-acetyl homoserine sulfhydrylase from Thermus thermophilus HB8
Authors: Imagawa, T. / Kousumi, Y. / Tsuge, H. / Utsunomiya, H. / Ebihara, A. / Nakagawa, N. / Yokoyama, S. / Kuramitsu, S.
History
DepositionMay 24, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-acetyl-L-homoserine sulfhydrylase
B: O-acetyl-L-homoserine sulfhydrylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7834
Polymers92,2892
Non-polymers4942
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-14 kcal/mol
Surface area33720 Å2
MethodPISA
2
A: O-acetyl-L-homoserine sulfhydrylase
B: O-acetyl-L-homoserine sulfhydrylase
hetero molecules

A: O-acetyl-L-homoserine sulfhydrylase
B: O-acetyl-L-homoserine sulfhydrylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,5668
Polymers184,5784
Non-polymers9894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Buried area23540 Å2
ΔGint-114 kcal/mol
Surface area49580 Å2
MethodPISA
3
A: O-acetyl-L-homoserine sulfhydrylase
hetero molecules

B: O-acetyl-L-homoserine sulfhydrylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7834
Polymers92,2892
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Buried area6740 Å2
ΔGint-23 kcal/mol
Surface area29820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.095, 149.095, 219.299
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 O-acetyl-L-homoserine sulfhydrylase


Mass: 46144.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: PET11a / Production host: Escherichia coli (E. coli)
References: UniProt: Q93I77, UniProt: Q5SK88*PLUS, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 3

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Sample preparation

CrystalDensity Matthews: 6.599191 Å3/Da / Density % sol: 81.361351 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.25% dichloromethane, 1.8M sodim/potassium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Type: SPRING-8 BEAMLINE / Wavelength: 0.9791, 0.9794, 0.9000
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 11, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
30.91
ReflectionResolution: 2.6→19.88 Å / Num. obs: 69366 / % possible obs: 100 % / Observed criterion σ(F): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.111
Reflection shellResolution: 2.6→2.666 Å / Rmerge(I) obs: 0.27 / Num. unique all: 5060 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→19.88 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.645 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.197 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21716 3690 5.1 %RANDOM
Rwork0.18706 ---
obs0.18857 69366 100 %-
all-73056 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.018 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6522 0 30 174 6726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0226722
X-RAY DIFFRACTIONr_angle_refined_deg2.5171.9619148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7625840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06623.401294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.001151066
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5051544
X-RAY DIFFRACTIONr_chiral_restr0.2060.21008
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025140
X-RAY DIFFRACTIONr_nbd_refined0.2670.23495
X-RAY DIFFRACTIONr_nbtor_refined0.3320.24497
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3190.2190
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.219
X-RAY DIFFRACTIONr_mcbond_it1.5141.54295
X-RAY DIFFRACTIONr_mcangle_it2.42826678
X-RAY DIFFRACTIONr_scbond_it3.75632789
X-RAY DIFFRACTIONr_scangle_it5.8744.52470
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 260 -
Rwork0.27 5060 -
obs--100 %

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