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- PDB-4ba4: Crystal structure of the apo omega-transaminase from Chromobacter... -

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Basic information

Entry
Database: PDB / ID: 4ba4
TitleCrystal structure of the apo omega-transaminase from Chromobacterium violaceum
ComponentsAMINOTRANSFERASE
KeywordsTRANSFERASE
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
Probable aminotransferase
Similarity search - Component
Biological speciesCHROMOBACTERIUM VIOLACEUM (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 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 1.2May 15, 2013Group: Other
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: AMINOTRANSFERASE
B: AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6553
Polymers102,5592
Non-polymers961
Water15,763875
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-70.1 kcal/mol
Surface area29680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.837, 61.897, 63.907
Angle α, β, γ (deg.)71.91, 86.99, 74.58
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.998, 0.062, 0.023), (0.047, 0.43, 0.902), (0.046, 0.901, -0.432)
Vector: 25.40965, -12.99831, 19.02801)

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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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 875 / 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: ROTATING ANODE / Wavelength: 1.54
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.73→14 Å / Num. obs: 74538 / % possible obs: 90.7 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.1
Reflection shellResolution: 1.73→1.82 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.4 / % possible all: 81.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QJ3

1qj3


Resolution: 1.73→60.75 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.391 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21826 3933 5 %RANDOM
Rwork0.17021 ---
obs0.17261 74538 90.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.868 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20.58 Å2-0.92 Å2
2---1.09 Å21.05 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.73→60.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6698 0 5 875 7578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197252
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9469875
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5375956
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69323.031353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.949151258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0831564
X-RAY DIFFRACTIONr_chiral_restr0.0880.21027
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215680
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.727→1.772 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 278 -
Rwork0.322 5192 -
obs--85.26 %

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