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- PDB-2z61: Crystal structure of MJ0684 from Methanococcus jannaschii reveals... -

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Basic information

Entry
Database: PDB / ID: 2z61
TitleCrystal structure of MJ0684 from Methanococcus jannaschii reveals its similarity in the active site to kynurenine aminotransferases
ComponentsProbable aspartate aminotransferase 2
KeywordsTRANSFERASE / amino acid aminotransferase / kynurenine aminotransferase / MJ0684 / Cytoplasm / Pyridoxal phosphate
Function / homology
Function and homology information


(5-formylfuran-3-yl)methyl phosphate transaminase / transaminase activity / biosynthetic process / pyridoxal phosphate binding / cytoplasm
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
(5-formylfuran-3-yl)methyl phosphate transaminase
Similarity search - Component
Biological speciesMethanococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.2 Å
AuthorsYang, J.K.
CitationJournal: BULL.KOREAN CHEM.SOC. / Year: 2008
Title: Crystal Structure of MJ0684 from Methanococcus jannaschii, a Novel Archaeal Homolog of Kynurenine Aminotransferase
Authors: Yang, J.K.
History
DepositionJul 21, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable aspartate aminotransferase 2


Theoretical massNumber of molelcules
Total (without water)42,6251
Polymers42,6251
Non-polymers00
Water1,56787
1
A: Probable aspartate aminotransferase 2

A: Probable aspartate aminotransferase 2


Theoretical massNumber of molelcules
Total (without water)85,2492
Polymers85,2492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5590 Å2
ΔGint-30 kcal/mol
Surface area28010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.866, 111.866, 60.862
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Probable aspartate aminotransferase 2 / MJ0684 protein / Transaminase A / ASPAT


Mass: 42624.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus jannaschii (archaea) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58097, aspartate transaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 20121 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 6.1 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 36.1
Reflection shellHighest resolution: 2.2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 4.3 / Rsym value: 0.407 / % possible all: 98.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.2→41.18 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 350372.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1943 9.9 %RANDOM
Rwork0.214 ---
obs0.214 19700 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.3932 Å2 / ksol: 0.294153 e/Å3
Displacement parametersBiso mean: 40.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å20 Å20 Å2
2---1.9 Å20 Å2
3---3.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→41.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2996 0 0 87 3083
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.821.5
X-RAY DIFFRACTIONc_mcangle_it2.82
X-RAY DIFFRACTIONc_scbond_it3.012
X-RAY DIFFRACTIONc_scangle_it4.452.5
LS refinement shellHighest resolution: 2.2 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.235 1943 -
Rwork0.214 0 -
obs-120856 99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1llp.paramllp.top
X-RAY DIFFRACTION2water.param

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