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- PDB-5vwr: E.coli Aspartate aminotransferase-(1R,3S,4S)-3-amino-4-fluorocycl... -

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Basic information

Entry
Database: PDB / ID: 5vwr
TitleE.coli Aspartate aminotransferase-(1R,3S,4S)-3-amino-4-fluorocyclopentane-1-carboxylic acid (FCP)-alpha-ketoglutarate
ComponentsAspartate aminotransferase
KeywordsTRANSFERASE / aspartate aminotransferase / Mechanism-based inactivator / ketimine / (1R / 3S / 4S)-3-amino-4-fluorocyclopentane-1-carboxylic acid (FCP) / alpha-ketoglutarate
Function / homology
Function and homology information


L-phenylalanine biosynthetic process / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine:2-oxoglutarate aminotransferase activity / aspartate catabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / 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 ...Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / 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
Chem-PL6 / Aspartate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.72 Å
AuthorsMascarenhas, R. / Liu, D. / Le, H. / Silverman, R.
CitationJournal: Biochemistry / Year: 2017
Title: Selective Targeting by a Mechanism-Based Inactivator against Pyridoxal 5'-Phosphate-Dependent Enzymes: Mechanisms of Inactivation and Alternative Turnover.
Authors: Mascarenhas, R. / Le, H.V. / Clevenger, K.D. / Lehrer, H.J. / Ringe, D. / Kelleher, N.L. / Silverman, R.B. / Liu, D.
History
DepositionMay 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Refinement description / Category: citation / software / Item: _citation.title
Revision 1.2Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Aspartate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4567
Polymers43,6191
Non-polymers8376
Water6,593366
1
A: Aspartate aminotransferase
hetero molecules

A: Aspartate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,91214
Polymers87,2382
Non-polymers1,67312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area8810 Å2
ΔGint-23 kcal/mol
Surface area28780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.400, 155.521, 77.409
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-791-

HOH

21A-794-

HOH

31A-882-

HOH

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Components

#1: Protein Aspartate aminotransferase / AspAT / Transaminase A


Mass: 43619.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: aspC, b0928, JW0911 / Production host: Escherichia coli (E. coli) / References: UniProt: P00509, aspartate transaminase
#2: Chemical ChemComp-PL6 / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-glutamic acid


Mass: 376.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17N2O9P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 25 mM potassium phosphate, 43% saturated ammonium sulfate

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 55946 / % possible obs: 99.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.027 / Rrim(I) all: 0.056 / Χ2: 0.873 / Net I/σ(I): 10.9 / Num. measured all: 240049
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.72-1.7540.9970.7010.530.80299.5
1.75-1.784.20.890.8010.4530.81399.5
1.78-1.824.30.7860.8570.3950.84599.60.883
1.82-1.854.30.6630.8820.3320.83399.50.744
1.85-1.894.30.5420.920.270.83399.60.608
1.89-1.944.30.440.9490.2190.88999.70.493
1.94-1.994.30.3450.9610.1720.88899.80.387
1.99-2.044.30.2650.9730.1330.91399.90.298
2.04-2.14.40.2060.9810.1030.92299.90.231
2.1-2.174.30.1650.9830.0830.9461000.185
2.17-2.244.30.1320.9860.0681.0471000.149
2.24-2.334.40.1120.9890.0571.0781000.126
2.33-2.444.40.090.9930.0460.9951000.101
2.44-2.574.30.0740.9950.0380.9371000.083
2.57-2.734.30.0620.9930.0320.9071000.07
2.73-2.944.30.0520.9940.0270.9241000.059
2.94-3.244.30.0450.9920.0240.9499.90.051
3.24-3.714.30.0360.9950.0190.931000.041
3.71-4.674.20.0250.9970.0130.54499.90.028
4.67-5040.0220.9980.0120.43696.60.025

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.72→34.744 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.87
RfactorNum. reflection% reflection
Rfree0.1904 2043 3.79 %
Rwork0.1669 --
obs0.1678 53898 49.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.76 Å2 / Biso mean: 25.2882 Å2 / Biso min: 7.17 Å2
Refinement stepCycle: final / Resolution: 1.72→34.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3056 0 55 366 3477
Biso mean--35.92 38.87 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073224
X-RAY DIFFRACTIONf_angle_d1.1384372
X-RAY DIFFRACTIONf_chiral_restr0.046479
X-RAY DIFFRACTIONf_plane_restr0.006573
X-RAY DIFFRACTIONf_dihedral_angle_d13.2871194
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.72-1.73220.3267750.2211825190026
1.7322-1.77550.27641010.22626272738
1.7755-1.82350.2061170.19153089320644
1.8235-1.87710.20171520.18763482363449
1.8771-1.93770.22411300.18263592372251
1.9377-2.0070.20551450.17793625377051
2.007-2.08730.22181390.16383625376452
2.0873-2.18230.19251470.16533626377352
2.1823-2.29730.18881500.15983629377952
2.2973-2.44120.18651420.16653669381152
2.4412-2.62970.20281430.16963630377352
2.6297-2.89420.16291390.16343677381652
2.8942-3.31270.17611530.16653691384453
3.3127-4.17250.16491490.14493838398754
4.1725-34.75120.19341610.17264231439260
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)
10.0812-0.0533-0.03670.01260.00630.0104-0.0185-0.0782-0.02980.06960.1337-0.0375-0.10180.142400.21280.00520.03580.211-0.01860.2043-20.5988-26.211715.0881
20.4914-0.0812-0.13520.19570.11430.32690.04310.1240.1056-0.0177-0.00090.0464-0.0246-0.07390.00440.08760.0066-0.00570.09890.02510.129-47.8322-17.502810.0705
30.1744-0.1647-0.06010.16630.06460.0379-0.03040.1565-0.2353-0.083-0.0371-0.0970.19110.007-0.00170.2021-0.00420.03480.1728-0.05180.1441-37.8428-38.6055-1.5319
40.9425-0.159-0.19710.4592-0.06420.10080.03660.25760.0311-0.0418-0.03210.07380.0394-0.10380.02960.0896-0.0149-0.02070.14280.00660.0643-47.5748-25.56572.5304
50.33470.41470.01570.59420.30280.5560.13510.26130.1411-0.26880.1259-0.2119-0.00880.04450.27420.13130.00230.06990.13690.00720.1026-23.7624-17.3198-5.0007
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 44 )A13 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 129 )A45 - 129
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 190 )A130 - 190
4X-RAY DIFFRACTION4chain 'A' and (resid 191 through 312 )A191 - 312
5X-RAY DIFFRACTION5chain 'A' and (resid 313 through 408 )A313 - 408

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