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- PDB-6dvs: Crystal structure of Pseudomonas stutzeri D-phenylglycine aminotr... -

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Basic information

Entry
Database: PDB / ID: 6dvs
TitleCrystal structure of Pseudomonas stutzeri D-phenylglycine aminotransferase
ComponentsD-phenylglycine aminotransferase
KeywordsTRANSFERASE / aminotransferase
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate binding
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
ACETATE ION / PHOSPHATE ION / Glutamate-1-semialdehyde 2,1-aminomutase
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.821 Å
AuthorsCouture, J.F. / Chica, R.
CitationJournal: Biochemistry / Year: 2018
Title: Structural Determinants of the Stereoinverting Activity of Pseudomonas stutzeri d-Phenylglycine Aminotransferase.
Authors: Walton, C.J.W. / Thiebaut, F. / Brunzelle, J.S. / Couture, J.F. / Chica, R.A.
History
DepositionJun 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-phenylglycine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,64021
Polymers49,1041
Non-polymers1,53520
Water4,720262
1
A: D-phenylglycine aminotransferase
hetero molecules

A: D-phenylglycine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,28042
Polymers98,2092
Non-polymers3,07140
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area12480 Å2
ΔGint-155 kcal/mol
Surface area31030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.639, 74.639, 149.948
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein D-phenylglycine aminotransferase


Mass: 49104.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: dpgA / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VY99, EC: 2.6.1.72

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Non-polymers , 6 types, 282 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 1 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→49.983 Å / Num. obs: 44043 / % possible obs: 99.8 % / Redundancy: 8.5 % / Net I/σ(I): 78.4
Reflection shellResolution: 1.82→2.04 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.821→49.983 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2223 2218 5.04 %
Rwork0.1788 --
obs0.181 44043 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.821→49.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3028 0 91 262 3381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063399
X-RAY DIFFRACTIONf_angle_d0.754622
X-RAY DIFFRACTIONf_dihedral_angle_d16.3681994
X-RAY DIFFRACTIONf_chiral_restr0.05502
X-RAY DIFFRACTIONf_plane_restr0.005612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8213-1.86090.36211130.27762582X-RAY DIFFRACTION100
1.8609-1.90420.26421450.24412587X-RAY DIFFRACTION100
1.9042-1.95180.26961170.21782569X-RAY DIFFRACTION100
1.9518-2.00460.27331220.20922562X-RAY DIFFRACTION100
2.0046-2.06360.26961360.19792620X-RAY DIFFRACTION100
2.0636-2.13020.23061620.19232548X-RAY DIFFRACTION100
2.1302-2.20630.22091350.18242605X-RAY DIFFRACTION100
2.2063-2.29470.21931410.18382575X-RAY DIFFRACTION100
2.2947-2.39910.24721280.18152619X-RAY DIFFRACTION100
2.3991-2.52560.20211380.18972591X-RAY DIFFRACTION100
2.5256-2.68380.21911340.18392609X-RAY DIFFRACTION100
2.6838-2.8910.23791730.18632590X-RAY DIFFRACTION100
2.891-3.18190.23271390.18442625X-RAY DIFFRACTION100
3.1819-3.64220.18171560.17172642X-RAY DIFFRACTION100
3.6422-4.58830.23371480.14292678X-RAY DIFFRACTION100
4.5883-50.00150.19051310.17412823X-RAY DIFFRACTION100

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