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- PDB-4wb0: Crystal structure of the broad specificity aminotransferase from ... -

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Basic information

Entry
Database: PDB / ID: 4wb0
TitleCrystal structure of the broad specificity aminotransferase from Leishmania mexicana
Components(Broad specificity aminotransferase) x 2
KeywordsTRANSFERASE / transamination / broad specificity / pyridoxal phosphate
Function / homology
Function and homology information


aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / amino acid metabolic process / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Aspartate/other aminotransferase / Aminotransferase, class I/classII / Aminotransferase class I and II / 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 ...Aspartate/other aminotransferase / Aminotransferase, class I/classII / Aminotransferase class I and II / 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
CACODYLATE ION / Aspartate transaminase
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsWen, J. / Nowicki, C. / Blankenfeldt, W.
CitationJournal: Mol.Biochem.Parasitol. / Year: 2015
Title: Structural basis for the relaxed substrate selectivity of Leishmania mexicana broad specificity aminotransferase.
Authors: Wen, J. / Nowicki, C. / Blankenfeldt, W.
History
DepositionSep 2, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Apr 25, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.3Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Broad specificity aminotransferase
B: Broad specificity aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2004
Polymers92,9262
Non-polymers2742
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-18 kcal/mol
Surface area29560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.418, 90.564, 142.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Broad specificity aminotransferase


Mass: 46470.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q71PB4
#2: Protein Broad specificity aminotransferase


Mass: 46454.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q71PB4
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 284 K / Method: vapor diffusion, hanging drop / Details: 1 M tri-sodium citrate, 0.1 M sodium cacodylate / PH range: 6.0 - 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9763 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.91→86.4 Å / Num. obs: 86628 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.4
Reflection shellResolution: 1.91→1.94 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2.1 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CST

2cst


Resolution: 1.91→76.381 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 20.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 4344 5.03 %
Rwork0.1766 --
obs0.1783 86399 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.91→76.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6318 0 10 474 6802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166579
X-RAY DIFFRACTIONf_angle_d1.4158959
X-RAY DIFFRACTIONf_dihedral_angle_d13.6882423
X-RAY DIFFRACTIONf_chiral_restr0.0691000
X-RAY DIFFRACTIONf_plane_restr0.0071159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.93170.30571230.26062691X-RAY DIFFRACTION97
1.9317-1.95440.23621330.24942693X-RAY DIFFRACTION99
1.9544-1.97830.311390.24612694X-RAY DIFFRACTION99
1.9783-2.00330.28661470.23982704X-RAY DIFFRACTION100
2.0033-2.02970.26621370.22752694X-RAY DIFFRACTION99
2.0297-2.05750.25881380.20662740X-RAY DIFFRACTION99
2.0575-2.08690.23621590.21122669X-RAY DIFFRACTION100
2.0869-2.1180.22821330.19652710X-RAY DIFFRACTION99
2.118-2.15110.20691380.19222736X-RAY DIFFRACTION100
2.1511-2.18640.24891430.19992693X-RAY DIFFRACTION99
2.1864-2.22410.24821390.1892732X-RAY DIFFRACTION99
2.2241-2.26460.22161340.18992695X-RAY DIFFRACTION99
2.2646-2.30810.26161570.18312718X-RAY DIFFRACTION100
2.3081-2.35520.20961440.18252701X-RAY DIFFRACTION99
2.3552-2.40640.22211220.17892754X-RAY DIFFRACTION99
2.4064-2.46240.21021660.18252696X-RAY DIFFRACTION99
2.4624-2.5240.21541420.17792719X-RAY DIFFRACTION99
2.524-2.59230.24091410.18372745X-RAY DIFFRACTION99
2.5923-2.66850.24161460.18222707X-RAY DIFFRACTION99
2.6685-2.75470.20081440.17692727X-RAY DIFFRACTION100
2.7547-2.85310.20211330.18552759X-RAY DIFFRACTION99
2.8531-2.96740.21311630.18482719X-RAY DIFFRACTION99
2.9674-3.10240.22861390.19082749X-RAY DIFFRACTION99
3.1024-3.2660.23911530.18812743X-RAY DIFFRACTION99
3.266-3.47060.22831390.17762779X-RAY DIFFRACTION99
3.4706-3.73860.17541580.16212744X-RAY DIFFRACTION99
3.7386-4.11480.19631530.15252778X-RAY DIFFRACTION99
4.1148-4.71010.16821560.13722784X-RAY DIFFRACTION100
4.7101-5.93390.17681490.15532851X-RAY DIFFRACTION100
5.9339-76.44240.1971760.17522931X-RAY DIFFRACTION99
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)
10.9047-0.51850.77133.99890.3320.69880.08350.5807-0.1334-0.4842-0.11210.00870.1244-0.04820.10060.3372-0.00780.06820.502-0.05880.2712-17.159418.1721-32.5768
23.94610.1127-0.80870.891-0.13691.3872-0.09520.189-0.10820.1514-0.02930.03620.0806-0.14460.09280.237-0.05080.00380.173-0.02570.1503-14.6617.6297-9.4851
32.9365-0.7712-0.02137.3905-5.4656.3663-0.06820.44770.492-0.10480.26580.50620.0102-0.7955-0.17630.2518-0.01550.00020.5006-0.0090.3295-38.936229.0766-11.3682
42.1796-0.1781-0.50911.0392-0.0481.0775-0.02790.05690.03830.08830.00130.07760.0185-0.14560.04030.2198-0.04080.01340.2055-0.0140.1655-21.459322.7685-5.2516
52.3779-0.23780.68292.3216-1.091.4961-0.13510.39410.5284-0.1580.07530.1743-0.1192-0.26980.05550.2220.01090.02070.36160.05320.2062-20.917635.746-24.7428
66.1891-3.06-1.35661.6937-0.21291.2092-0.3033-0.3397-1.00920.2725-0.03710.20020.09320.12650.36820.3517-0.0937-0.02620.2625-0.10520.3448-1.45774.1315-1.2391
71.8640.10880.1693.41880.54791.01370.06160.3112-0.52140.0744-0.21650.0760.3904-0.04390.08450.3757-0.05330.03620.2899-0.12590.3033-5.3655-1.8239-23.5459
81.4774-0.3434-0.13671.7301-0.04471.29850.06970.3428-0.4023-0.2139-0.1626-0.16560.36920.15740.09470.34360.01850.04430.3063-0.08590.30542.3031-1.339-26.0152
92.54020.08860.40262.12850.02842.58520.2188-0.2933-0.65990.0967-0.7337-0.98270.76740.4410.37320.5640.0682-0.04380.37050.15950.666214.3724-11.3717-3.6579
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 158 )
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 178 )
4X-RAY DIFFRACTION4chain 'A' and (resid 179 through 291 )
5X-RAY DIFFRACTION5chain 'A' and (resid 292 through 410 )
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 56 )
7X-RAY DIFFRACTION7chain 'B' and (resid 57 through 188 )
8X-RAY DIFFRACTION8chain 'B' and (resid 189 through 342 )
9X-RAY DIFFRACTION9chain 'B' and (resid 343 through 408 )

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