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- PDB-2z9u: Crystal structure of pyridoxamine-pyruvate aminotransferase from ... -

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Basic information

Entry
Database: PDB / ID: 2z9u
TitleCrystal structure of pyridoxamine-pyruvate aminotransferase from Mesorhizobium loti at 2.0 A resolution
ComponentsAspartate aminotransferase
KeywordsTRANSFERASE / AMINOTRANSFERASE / PYRIDOXAMINE / PYRUVATE
Function / homology
Function and homology information


pyridoxamine-pyruvate transaminase / pyridoxamine-pyruvate transaminase activity / L-serine-pyruvate transaminase activity / glycine biosynthetic process, by transamination of glyoxylate / alanine-glyoxylate transaminase activity / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class V domain / Aminotransferase class-V / 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 ...Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class V domain / Aminotransferase class-V / 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
Pyridoxamine--pyruvate transaminase
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYoshikane, Y. / Yokochi, N. / Yamasaki, M. / Mizutani, K. / Ohnishi, K. / Mikami, B. / Hayashi, H. / Yagi, T.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of pyridoxamine-pyruvate aminotransferase from Mesorhizobium loti MAFF303099
Authors: Yoshikane, Y. / Yokochi, N. / Yamasaki, M. / Mizutani, K. / Ohnishi, K. / Mikami, B. / Hayashi, H. / Yagi, T.
History
DepositionSep 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Aspartate aminotransferase
B: Aspartate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,95212
Polymers83,0072
Non-polymers94510
Water9,908550
1
A: Aspartate aminotransferase
B: Aspartate aminotransferase
hetero molecules

A: Aspartate aminotransferase
B: Aspartate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,90424
Polymers166,0144
Non-polymers1,89020
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area17630 Å2
ΔGint-261 kcal/mol
Surface area48190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.545, 68.545, 311.635
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 Aspartate aminotransferase / Pyridoxamine-pyruvate aminotransferase


Mass: 41503.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Strain: MAFF303099 / Gene: mlr6806 / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q988B8, pyridoxamine-pyruvate transaminase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.2 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.05
Details: 0.1M HEPES, 2M Ammonium sulfate, pH 8.05, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Apr 10, 2006
RadiationMonochromator: DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 58804 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 18.89 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.379 / Num. unique all: 5701 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1VJO

1vjo


Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.669 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20553 2551 5.1 %RANDOM
Rwork0.15558 ---
obs0.15809 47892 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.596 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5832 0 54 550 6436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226132
X-RAY DIFFRACTIONr_angle_refined_deg1.441.988381
X-RAY DIFFRACTIONr_chiral_restr0.0990.2948
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024634
X-RAY DIFFRACTIONr_nbd_refined0.1980.23094
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24216
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2569
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.224
X-RAY DIFFRACTIONr_mcbond_it0.7291.54071
X-RAY DIFFRACTIONr_mcangle_it1.11926358
X-RAY DIFFRACTIONr_scbond_it2.10632374
X-RAY DIFFRACTIONr_scangle_it3.2244.52012
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 196 -
Rwork0.18 3441 -
obs-3441 98.14 %

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