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- PDB-4wd2: Crystal structure of an aromatic amino acid aminotransferase from... -

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Basic information

Entry
Database: PDB / ID: 4wd2
TitleCrystal structure of an aromatic amino acid aminotransferase from Burkholderia cenocepacia J2315
ComponentsAromatic-amino-acid transaminase TyrB
KeywordsTRANSFERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyAspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesBurkholderia cenocepacia K56-2Valvano (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of an aromatic amino acid aminotransferase from Burkholderia cenocepacia J2315
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionSep 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 2.0Nov 22, 2017Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _entity.formula_weight / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 2.2Nov 15, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / struct_ref
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aromatic-amino-acid transaminase TyrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2575
Polymers44,8891
Non-polymers3684
Water7,134396
1
A: Aromatic-amino-acid transaminase TyrB
hetero molecules

A: Aromatic-amino-acid transaminase TyrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,51410
Polymers89,7772
Non-polymers7378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556x,x-y,-z+11
Buried area8040 Å2
ΔGint-29 kcal/mol
Surface area28180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.220, 59.220, 200.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-735-

HOH

DetailsThe biological unit is a dimer generated from the monomer in the asymmetric unit by the crystallographic operations x,x-y,-z+1

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Components

#1: Protein Aromatic-amino-acid transaminase TyrB


Mass: 44888.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia K56-2Valvano (bacteria)
Gene: tyrB, BURCENK562V_C3553 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: T0EWC0, aromatic-amino-acid transaminase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: Rigaku Reagents JCSG+ screen d1: 24% PEG 1500, 20% glycerol; BuceA.01471.a.B1.PS01824 at 20 mg/ml + 2.5mM pyridoxal phosphate; di rect cryo; tray 257500 d1, puck zba1-4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 25, 2014
RadiationMonochromator: Rigaku VariMax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.27
ReflectionResolution: 1.95→50 Å / Num. obs: 29633 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 9.86 % / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.095 / Χ2: 0.909 / Net I/σ(I): 22.52 / Num. measured all: 292285
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.95-24.80.8670.3464.729510218419860.38790.9
2-2.060.9110.3076.0712281213620660.33696.7
2.06-2.120.9420.2857.8915599209220880.30699.8
2.12-2.180.970.24710.6820200199819980.261100
2.18-2.250.980.20713.1620856193819380.217100
2.25-2.330.9850.19313.7520421188918890.203100
2.33-2.420.9880.1715.4919996182618260.179100
2.42-2.520.990.15816.5319344177317730.165100
2.52-2.630.9920.13419.1418478167716770.14100
2.63-2.760.9940.12420.3817769162816280.13100
2.76-2.910.9960.10323.9216958153215320.108100
2.91-3.080.9970.08328.3716381148414840.087100
3.08-3.30.9980.06933.0615260138213820.073100
3.3-3.560.9990.05442.2714056127012680.05799.8
3.56-3.90.9990.04649.2413086119511950.048100
3.9-4.360.9990.04450.811855107910790.046100
4.36-5.030.9990.04153.13106659719710.043100
5.03-6.170.9990.0543.3188738158150.053100
6.17-8.720.9990.04447.5569886546530.04699.8
8.720.9990.03161.6137093923850.03398.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.5.7phasing
PHENIX(phenix.refine: dev_1779)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3tat

3tat


Resolution: 1.95→45.647 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.36 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1514 1497 5.06 %Random selection
Rwork0.1156 28055 --
obs0.1183 29568 99.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.85 Å2 / Biso mean: 16.3048 Å2 / Biso min: 5.81 Å2
Refinement stepCycle: final / Resolution: 1.95→45.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3009 0 24 396 3429
Biso mean--31.45 24.81 -
Num. residues----398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053124
X-RAY DIFFRACTIONf_angle_d0.8934245
X-RAY DIFFRACTIONf_chiral_restr0.035468
X-RAY DIFFRACTIONf_plane_restr0.003556
X-RAY DIFFRACTIONf_dihedral_angle_d12.6021122
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9507-2.01370.17931260.14872323244987
2.0137-2.08560.19121290.13842498262793
2.0856-2.16910.18141350.12812563269895
2.1691-2.26780.16571370.12092567270495
2.2678-2.38730.12891310.11752535266695
2.3873-2.53680.1531360.11782549268595
2.5368-2.73260.16041410.11552561270295
2.7326-3.00740.15061340.11272580271495
3.0074-3.44210.15611390.11142586272595
3.4421-4.33490.12711360.10082592272895
4.3349-31.57160.14171410.1162701284295
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)
10.0053-0.00140.0174-0.0004-0.00490.0265-0.0062-0.05930.12030.0467-0.08560.0007-0.0885-0.10780.10290.20120.01860.01280.1974-0.00280.1614-9.407622.844797.8074
21.6166-0.55941.08780.6427-0.32890.79270.041-0.0331-0.14060.1050.05740.14150.0062-0.1319-0.09530.12220.01910.03690.12950.01330.1305-11.6792-4.627693.1716
30.44030.2752-0.07160.8994-0.14581.02890.020.00460.04940.06850.0264-0.0244-0.12340.0627-0.050.06440.01480.00590.0833-0.01570.08419.59226.506883.4621
40.29990.03020.08320.22-0.11480.7214-0.0012-0.007-0.00710.00980.0063-0.00140.0114-0.0019-0.0030.07740.0122-0.00230.0528-0.01470.08210.29170.560481.0743
51.215-0.1953-0.23582.9840.63821.5610.04480.06180.0157-0.1789-0.0163-0.0971-0.1652-0.1327-0.02440.11160.0433-0.00860.1188-0.02530.1213-10.664523.090175.9999
61.0763-0.45680.42360.90350.1480.83840.00180.02220.0931-0.0606-0.05180.0182-0.1323-0.04530.04030.13840.04660.00150.1108-0.00720.1134-16.832723.491378.6316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 32 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 71 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 178 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 179 through 330 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 331 through 363 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 364 through 400 )A0

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