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- PDB-4a6r: Crystal structure of the omega transaminase from Chromobacterium ... -

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Basic information

Entry
Database: PDB / ID: 4a6r
TitleCrystal structure of the omega transaminase from Chromobacterium violaceum in the apo form, crystallised from polyacrylic acid
ComponentsOMEGA TRANSAMINASE
KeywordsTRANSFERASE / PLP-BINDING ENZYME / TRANSAMINASE FOLD TYPE I
Function / homology
Function and homology information


adenosylmethionine-8-amino-7-oxononanoate transaminase / 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
POLYACRYLIC ACID / Probable aminotransferase
Similarity search - Component
Biological speciesCHROMOBACTERIUM VIOLACEUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.349 Å
AuthorsLogan, D.T. / Hakansson, M. / Yengo, K. / Svedendahl Humble, M. / Engelmark Cassimjee, K. / Walse, B. / Abedi, V. / Federsel, H.-J. / Berglund, P.
CitationJournal: FEBS J. / Year: 2012
Title: Crystal Structures of the Chromobacterium Violaceum Omega-Transaminase Reveal Major Structural Rearrangements Upon Binding of Coenzyme Plp.
Authors: Svedendahl Humble, M. / Engelmark Cassimjee, K. / Hakansson, M. / Kimbung, Y.R. / Walse, B. / Abedi, V. / Federsel, H.-J. / Berglund, P. / Logan, D.T.
History
DepositionNov 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 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

Downloads & links

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Assembly

Deposited unit
A: OMEGA TRANSAMINASE
B: OMEGA TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,1394
Polymers102,5592
Non-polymers5812
Water15,169842
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-47 kcal/mol
Surface area29660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.590, 61.870, 63.540
Angle α, β, γ (deg.)108.03, 87.31, 105.16
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9972, -0.05709, 0.04849), (-0.06842, 0.4309, -0.8998), (0.03047, -0.9006, -0.4336)
Vector: 65.81, 34.71, 50.55)

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Components

#1: Protein OMEGA TRANSAMINASE / PROBABLE 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(DE3)
References: UniProt: Q7NWG4, beta-alanine-pyruvate transaminase, adenosylmethionine-8-amino-7-oxononanoate transaminase
#2: Chemical ChemComp-TA8 / POLYACRYLIC ACID / OCTANE-1,3,5,7-TETRACARBOXYLIC ACID


Mass: 290.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 842 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPOLYACRYLIC ACID (TA8): POLYACRYLIC ACID (N=3)

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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: 2.05 Å3/Da / Density % sol: 39.9 % / Description: NONE
Crystal growpH: 7.4
Details: 0.2 M MGCL2, 0.1 M HEPES PH 7.5, 22% W/V POLYACRYLIC ACID 5100 SODIUM SALT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0397
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Apr 16, 2011 / Details: MULTILAYER MIRROR, VERTICALLY FOCUSING
RadiationMonochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0397 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 690977 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 10.87 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.6
Reflection shellResolution: 1.35→1.38 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.9 / % possible all: 89.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HMU

3hmu


Resolution: 1.349→23.287 Å / SU ML: 0.15 / σ(F): 1.99 / Phase error: 15.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1627 8516 5 %
Rwork0.1335 --
obs0.135 169719 94.17 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.043 Å2 / ksol: 0.39 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9941 Å20.7765 Å20.2733 Å2
2--0.0858 Å20.4737 Å2
3---0.9082 Å2
Refinement stepCycle: LAST / Resolution: 1.349→23.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6640 0 40 842 7522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086924
X-RAY DIFFRACTIONf_angle_d1.2199386
X-RAY DIFFRACTIONf_dihedral_angle_d13.0982522
X-RAY DIFFRACTIONf_chiral_restr0.071984
X-RAY DIFFRACTIONf_plane_restr0.0071232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.349-1.36430.35182670.29944957X-RAY DIFFRACTION86
1.3643-1.38040.26462730.22125269X-RAY DIFFRACTION92
1.3804-1.39720.25092740.20795151X-RAY DIFFRACTION91
1.3972-1.41490.26842780.19365279X-RAY DIFFRACTION92
1.4149-1.43350.22152800.18865243X-RAY DIFFRACTION92
1.4335-1.45310.24162850.1825246X-RAY DIFFRACTION92
1.4531-1.47390.21182640.16545375X-RAY DIFFRACTION92
1.4739-1.49590.1892880.1525198X-RAY DIFFRACTION92
1.4959-1.51930.19562610.14335315X-RAY DIFFRACTION93
1.5193-1.54420.17572930.13455304X-RAY DIFFRACTION93
1.5442-1.57080.17192870.12785276X-RAY DIFFRACTION94
1.5708-1.59930.15722730.12145360X-RAY DIFFRACTION94
1.5993-1.63010.15632870.11325356X-RAY DIFFRACTION93
1.6301-1.66330.16152940.11465322X-RAY DIFFRACTION94
1.6633-1.69950.17253020.11435345X-RAY DIFFRACTION94
1.6995-1.7390.16323100.11465339X-RAY DIFFRACTION94
1.739-1.78250.15572780.10895458X-RAY DIFFRACTION95
1.7825-1.83070.14222710.10435401X-RAY DIFFRACTION94
1.8307-1.88450.13622990.11065399X-RAY DIFFRACTION95
1.8845-1.94530.14892850.11255436X-RAY DIFFRACTION95
1.9453-2.01480.15492850.11555408X-RAY DIFFRACTION95
2.0148-2.09540.15982820.11555477X-RAY DIFFRACTION96
2.0954-2.19070.15072750.1145514X-RAY DIFFRACTION96
2.1907-2.30610.1432620.11085521X-RAY DIFFRACTION96
2.3061-2.45050.14312840.11565523X-RAY DIFFRACTION96
2.4505-2.63940.13762910.12235512X-RAY DIFFRACTION97
2.6394-2.90460.16572840.13455550X-RAY DIFFRACTION97
2.9046-3.32390.16592740.14215590X-RAY DIFFRACTION98
3.3239-4.18380.153230.13675542X-RAY DIFFRACTION98
4.1838-23.290.14273070.14875537X-RAY DIFFRACTION97

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