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- PDB-4h51: Crystal structure of a putative Aspartate Aminotransferase from L... -

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Basic information

Entry
Database: PDB / ID: 4h51
TitleCrystal structure of a putative Aspartate Aminotransferase from Leishmania major Friedlin
ComponentsAspartate aminotransferase
KeywordsTRANSFERASE / SSGCID / Leishmania major / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / Aspartate aminotransferase / 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
Aspartate transaminase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Structures of aspartate aminotransferases from Trypanosoma brucei, Leishmania major and Giardia lamblia.
Authors: Abendroth, J. / Choi, R. / Wall, A. / Clifton, M.C. / Lukacs, C.M. / Staker, B.L. / Van Voorhis, W. / Myler, P. / Lorimer, D.D. / Edwards, T.E.
History
DepositionSep 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2May 20, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate aminotransferase
B: Aspartate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7274
Polymers94,6032
Non-polymers1242
Water13,637757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-26 kcal/mol
Surface area28060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.410, 93.670, 74.590
Angle α, β, γ (deg.)90.000, 106.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aspartate aminotransferase / Putative aspartate aminotransferase


Mass: 47301.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin / Gene: asat, LMJF_24_0370, LMJF_35_0820 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4FX34, aspartate transaminase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 757 / 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: 2.19 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: EmeraldBio PACT screen e12: 20% PEG 3350, 200mM NaMalonate pH 7.0, LemaA.01471.b.B1.PS00838 at 19mg/ml with 2.5mM PLP, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 22, 2012 / Details: RIGAKU VARIMAX
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 69108 / Num. obs: 68837 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 25.426 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 22.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
1.85-1.90.5412.26153705102503798.7
1.9-1.950.422.99153784966492799.2
1.95-2.010.3123.96157654843483499.8
2.01-2.070.2465.23155474663463499.4
2.07-2.140.2046.69162054543451099.3
2.14-2.210.1639.72189034402439699.9
2.21-2.290.14112.53197034242420399.1
2.29-2.390.12114.392047540964096100
2.39-2.490.10416.8206313936392899.8
2.49-2.620.09119.212079237183717100
2.62-2.760.07823.33217823579357599.9
2.76-2.930.06528.82242583394338999.9
2.93-3.130.05334.772392731783178100
3.13-3.380.04142.852214029352934100
3.38-3.70.03254.63203362726272499.9
3.7-4.140.02765.5184722483247399.6
4.14-4.780.02472.361639821882188100
4.78-5.850.02665.02138961844184299.9
5.85-8.270.02764.24107791448144299.6
8.27-500.01890.49573682281098.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.93 Å
Translation3.5 Å19.93 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.1843 / WRfactor Rwork: 0.1465 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8688 / SU B: 5.665 / SU ML: 0.089 / SU R Cruickshank DPI: 0.1375 / SU Rfree: 0.1318 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 3471 5 %RANDOM
Rwork0.1675 ---
obs0.1698 68814 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 max: 50.73 Å2 / Biso mean: 19.923 Å2 / Biso min: 7.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20.28 Å2
2---0.17 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6221 0 8 757 6986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.026442
X-RAY DIFFRACTIONr_bond_other_d0.0010.024242
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.9628782
X-RAY DIFFRACTIONr_angle_other_deg0.993310347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0365824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07723.902287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.975151031
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.031541
X-RAY DIFFRACTIONr_chiral_restr0.0920.2987
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217263
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021328
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 244 -
Rwork0.274 4697 -
all-4941 -
obs--98.72 %
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)
10.4333-0.2438-0.00380.50940.09470.3212-0.0323-0.03890.02570.0422-0.00350.046-0.0228-0.05670.03580.0294-0.00560.01190.0237-0.02360.034138.40110.35960.875
20.5208-0.0296-0.15660.8638-0.08020.37310.0291-0.0242-0.0628-0.0354-0.072-0.0702-0.01350.04910.04290.0184-0.01050.01090.03360.00460.024459.371-14.95449.654
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 407
2X-RAY DIFFRACTION1A500
3X-RAY DIFFRACTION2B7 - 409
4X-RAY DIFFRACTION2B500

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