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- PDB-4m0j: Crystal structure of a D-amino acid aminotransferase from Burkhol... -

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Basic information

Entry
Database: PDB / ID: 4m0j
TitleCrystal structure of a D-amino acid aminotransferase from Burkholderia thailandensis E264
ComponentsD-amino acid aminotransferase
KeywordsTRANSFERASE / NIAID / SSGCID / Structural Genomics / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / D-amino acid aminotransferase
Function / homology
Function and homology information


carboxylic acid biosynthetic process / transaminase activity / metal ion binding / cytosol
Similarity search - Function
: / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 ...: / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
D-amino acid aminotransferase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a D-amino acid aminotransferase from Burkholderia thailandensis E264
Authors: Lukacs, C.M. / Edwards, T.E. / Lorimer, D.
History
DepositionAug 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: D-amino acid aminotransferase
B: D-amino acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0673
Polymers68,0272
Non-polymers401
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-33 kcal/mol
Surface area23780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.600, 73.980, 76.210
Angle α, β, γ (deg.)90.00, 105.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-401-

CA

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Components

#1: Protein D-amino acid aminotransferase


Mass: 34013.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH_I0381 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2T1L0
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG4000, 0.2M Cacl2, 0.1M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9798 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 39005 / % possible obs: 99.6 % / Redundancy: 3.74 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 19.8
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 3.76 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 3.18 / Num. unique all: 2863 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DAA

1daa


Resolution: 2.05→44.19 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.07 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22374 1943 5 %RANDOM
Rwork0.17909 ---
obs0.18141 36949 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.062 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å2-0.19 Å2
2--0.05 Å2-0 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.05→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4228 0 1 298 4527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194319
X-RAY DIFFRACTIONr_bond_other_d0.0010.024160
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9645894
X-RAY DIFFRACTIONr_angle_other_deg0.7939502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9575568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45923.591181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32315645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2191534
X-RAY DIFFRACTIONr_chiral_restr0.0920.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214982
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02948
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_it1.962.6282284
X-RAY DIFFRACTIONr_mcbond_other1.9592.6272283
X-RAY DIFFRACTIONr_mcangle_it2.9143.9242848
X-RAY DIFFRACTIONr_mcangle_other2.9143.9252849
X-RAY DIFFRACTIONr_scbond_it2.4042.8722035
X-RAY DIFFRACTIONr_scbond_other2.4042.8732036
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6594.2093047
X-RAY DIFFRACTIONr_long_range_B_refined5.80221.5684866
X-RAY DIFFRACTIONr_long_range_B_other5.7221.194751
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 155 -
Rwork0.226 2702 -
obs--99.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3156-0.3322-0.03530.88010.07360.52620.0172-0.06720.0862-0.1528-0.0171-0.1976-0.01630.078-00.0989-0.02380.05380.0614-0.00810.09736.11976.70658.8743
20.9004-0.47910.12780.3476-0.12330.88490.0162-0.0886-0.046-0.00010.01940.00530.0787-0.1323-0.03560.0631-0.0534-0.01720.06330.02610.02998.7806-0.243524.8498
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 300
2X-RAY DIFFRACTION2B6 - 300

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