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- PDB-4ba5: Crystal structure of omega-transaminase from Chromobacterium violaceum -

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Basic information

Entry
Database: PDB / ID: 4ba5
TitleCrystal structure of omega-transaminase from Chromobacterium violaceum
ComponentsAMINOTRANSFERASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


adenosylmethionine-8-amino-7-oxononanoate transaminase activity / pyridoxal phosphate binding / identical protein binding / cytosol
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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
3-[O-PHOSPHONOPYRIDOXYL]--AMINO-BENZOIC ACID / Putative 8-amino-7-oxononanoate synthase
Similarity search - Component
Biological speciesCHROMOBACTERIUM VIOLACEUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsSayer, C. / Isupov, M.N. / Littlechild, J.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural Studies with Pseudomonas and Chromobacterium [Omega]-Aminotransferases Provide Insights Into Their Differing Substrate Specificity.
Authors: Sayer, C. / Isupov, M.N. / Westlake, A. / Littlechild, J.A.
History
DepositionSep 11, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Dec 20, 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_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_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: AMINOTRANSFERASE
B: AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3915
Polymers102,5592
Non-polymers8333
Water10,485582
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-60.3 kcal/mol
Surface area28480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.452, 60.536, 61.300
Angle α, β, γ (deg.)68.40, 76.18, 84.28
Int Tables number1
Space group name H-MP1

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Components

#1: Protein AMINOTRANSFERASE


Mass: 51279.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHROMOBACTERIUM VIOLACEUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q7NWG4, beta-alanine-pyruvate transaminase
#2: Chemical ChemComp-PXG / 3-[O-PHOSPHONOPYRIDOXYL]--AMINO-BENZOIC ACID


Mass: 368.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H17N2O7P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 2.08 Å3/Da / Density % sol: 40.4 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.49
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.49 Å / Relative weight: 1
ReflectionResolution: 1.73→41.7 Å / Num. obs: 65355 / % possible obs: 86.6 % / Observed criterion σ(I): 1.7 / Redundancy: 2.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.8
Reflection shellResolution: 1.73→1.82 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 1.7 / % possible all: 52.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AH3

4ah3


Resolution: 1.76→56.75 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.17 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2325 135 2 %RANDOM
Rwork0.17363 ---
obs0.1747 65355 88.85 %-
Displacement parametersBiso mean: 31.192 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0.51 Å21.27 Å2
2--0.34 Å2-0.47 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.76→56.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6702 0 55 582 7339
LS refinement shellResolution: 1.761→1.807 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 65 -
Rwork0.376 2910 -
obs--53.82 %

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