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- PDB-3g7q: Crystal structure of valine-pyruvate aminotransferase AvtA (NP_46... -

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Basic information

Entry
Database: PDB / ID: 3g7q
TitleCrystal structure of valine-pyruvate aminotransferase AvtA (NP_462565.1) from Salmonella typhimurium LT2 at 1.80 A resolution
ComponentsValine-pyruvate aminotransferase
KeywordsTRANSFERASE / NP_462565.1 / valine-pyruvate aminotransferase AvtA / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Aminotransferase / Pyruvate
Function / homology
Function and homology information


valine-pyruvate transaminase / valine-pyruvate transaminase activity / alpha-amino acid metabolic process / valine biosynthetic process / transaminase activity / pyridoxal phosphate binding / cytosol
Similarity search - Function
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, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Valine-pyruvate aminotransferase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of valine-pyruvate aminotransferase AvtA (NP_462565.1) from Salmonella typhimurium LT2 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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: Valine-pyruvate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7347
Polymers47,4411
Non-polymers2936
Water5,008278
1
A: Valine-pyruvate aminotransferase
hetero molecules

A: Valine-pyruvate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,46714
Polymers94,8822
Non-polymers58512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area3100 Å2
ΔGint-18.1 kcal/mol
Surface area29280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.280, 92.280, 227.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-418-

CL

DetailsTHE RESULTS FROM SIZE EXCLUSION CHROMATOGRAPHY SUPPORT THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Valine-pyruvate aminotransferase


Mass: 47441.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / Gene: avtA, NP_462565.1, STM3665 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8ZL86, valine-pyruvate transaminase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.94 Å3/Da / Density % sol: 58.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: NANODROP, 40.0% Ethylene glycol, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97874, 0.97828
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 12, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978741
30.978281
ReflectionResolution: 1.8→29.285 Å / Num. obs: 53916 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 28.602 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.25
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.860.9431.8447349237198.2
1.86-1.940.6122.753645108011100
1.94-2.030.414.15181710183199.9
2.03-2.130.2676.1488159405199.9
2.13-2.270.1868.756148105261100
2.27-2.440.13411.8535029780199.9
2.44-2.690.115.557727102271100
2.69-3.070.06921.85784898611100
3.07-3.870.04731.361805101491100
3.87-29.290.0438.26226510123199.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.28 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 3.953 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.094
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.CHLORIDE IONS AND ETHYLENE GLYCOL MOLECULE FROM CRYSTALLIZATION ARE MODELED IN THIS STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.19577 2733 5.1 %RANDOM
Rwork0.17797 ---
obs0.17886 53818 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 84.56 Å2 / Biso mean: 29.685 Å2 / Biso min: 14.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2976 0 15 278 3269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223304
X-RAY DIFFRACTIONr_bond_other_d0.0020.022232
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.9754519
X-RAY DIFFRACTIONr_angle_other_deg1.01835471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9455435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89324.286140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.36715548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6271519
X-RAY DIFFRACTIONr_chiral_restr0.0760.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023805
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02656
X-RAY DIFFRACTIONr_nbd_refined0.2290.3722
X-RAY DIFFRACTIONr_nbd_other0.1830.32340
X-RAY DIFFRACTIONr_nbtor_refined0.180.51672
X-RAY DIFFRACTIONr_nbtor_other0.0850.51605
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.5420
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.318
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.350
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.531
X-RAY DIFFRACTIONr_mcbond_it1.80632159
X-RAY DIFFRACTIONr_mcbond_other0.4243831
X-RAY DIFFRACTIONr_mcangle_it2.67753383
X-RAY DIFFRACTIONr_scbond_it4.47881319
X-RAY DIFFRACTIONr_scangle_it6.383111136
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 220 -
Rwork0.223 3658 -
all-3878 -
obs--98.65 %
Refinement TLS params.Method: refined / Origin x: -26.0867 Å / Origin y: 59.999 Å / Origin z: 14.1651 Å
111213212223313233
T-0.0137 Å20.0104 Å20.0222 Å2--0.0989 Å2-0.0165 Å2---0.0439 Å2
L0.7464 °2-0.2478 °20.2536 °2-0.7419 °2-0.1505 °2--0.854 °2
S-0.0484 Å °-0.044 Å °-0.1681 Å °0.0614 Å °0.0671 Å °0.0473 Å °0.1156 Å °-0.061 Å °-0.0186 Å °

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