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- PDB-1dju: CRYSTAL STRUCTURE OF AROMATIC AMINOTRANSFERASE FROM PYROCOCCUS HO... -

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Basic information

Entry
Database: PDB / ID: 1dju
TitleCRYSTAL STRUCTURE OF AROMATIC AMINOTRANSFERASE FROM PYROCOCCUS HORIKOSHII OT3
ComponentsAROMATIC AMINOTRANSFERASE
KeywordsTRANSFERASE / ALPHA/BETA/ALPHA
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / 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 ...Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / 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 / Aminotransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsMatsui, I. / Matsui, E. / Sakai, Y. / Kikuchi, H. / Kawarabayashi, H.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: The molecular structure of hyperthermostable aromatic aminotransferase with novel substrate specificity from Pyrococcus horikoshii.
Authors: Matsui, I. / Matsui, E. / Sakai, Y. / Kikuchi, H. / Kawarabayasi, Y. / Ura, H. / Kawaguchi, S. / Kuramitsu, S. / Harata, K.
History
DepositionDec 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AROMATIC AMINOTRANSFERASE
B: AROMATIC AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1824
Polymers87,6872
Non-polymers4942
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-24 kcal/mol
Surface area26400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.010, 124.870, 128.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AROMATIC AMINOTRANSFERASE


Mass: 43843.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Production host: Escherichia coli (E. coli) / References: UniProt: O59096
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1,6-HEXANE-DI-OL, MAGNESIUM CHLORIDE, PYRIDOXAL-5'-PHOSPHATE, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13 M1,6-hexane-di-ol1drop
2100 mMHEPES1drop
310 mM1dropMgCl2
41.6 %ArATPh1drop
50.02 mMpyridoxal-5'-phosphate1drop
63 M1,6-hexane-di-ol1reservoir

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Data collection

DiffractionMean temperature: 286 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 10, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→28 Å / Num. all: 57422 / Num. obs: 57422 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.046
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.184 / % possible all: 70.1
Reflection
*PLUS
Num. measured all: 359213
Reflection shell
*PLUS
% possible obs: 70.1 %

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Processing

Software
NameVersionClassification
MIRPHSmodel building
X-PLOR3.1refinement
MADNESSdata reduction
MERGEFdata scaling
MIRPHSphasing
RefinementResolution: 2.1→8 Å / σ(F): 2 / Stereochemistry target values: CHARMM BY BROOKS ET AL. / Details: ENERGY MINIMIZATION
RfactorNum. reflectionSelection details
Rfree0.254 2873 RANDOM
Rwork0.185 --
obs0.185 47508 -
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5952 0 30 200 6182
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.24
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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