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- PDB-5wmi: Arabidopsis thaliana Prephenate Aminotransferase mutant- T84V -

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Basic information

Entry
Database: PDB / ID: 5wmi
TitleArabidopsis thaliana Prephenate Aminotransferase mutant- T84V
ComponentsBifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
KeywordsTRANSFERASE / aspartate aminotransferase / PLP-dependent
Function / homology
Function and homology information


glutamate-prephenate aminotransferase / glutamate-prephenate aminotransferase activity / aromatic amino acid family biosynthetic process, prephenate pathway / aspartate-prephenate aminotransferase / aspartate-prephenate aminotransferase activity / embryo development ending in seed dormancy / L-phenylalanine biosynthetic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / chloroplast stroma ...glutamate-prephenate aminotransferase / glutamate-prephenate aminotransferase activity / aromatic amino acid family biosynthetic process, prephenate pathway / aspartate-prephenate aminotransferase / aspartate-prephenate aminotransferase activity / embryo development ending in seed dormancy / L-phenylalanine biosynthetic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / chloroplast stroma / chloroplast / pyridoxal phosphate binding
Similarity search - Function
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 ...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
2-OXOGLUTARIC ACID / Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJez, J.M. / Holland, C.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB--1157771 United States
CitationJournal: Plant J. / Year: 2018
Title: Structural basis for substrate recognition and inhibition of prephenate aminotransferase from Arabidopsis.
Authors: Holland, C.K. / Berkovich, D.A. / Kohn, M.L. / Maeda, H. / Jez, J.M.
History
DepositionJul 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1982
Polymers51,0511
Non-polymers1461
Water2,612145
1
A: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
hetero molecules

A: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3954
Polymers102,1032
Non-polymers2922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area6770 Å2
ΔGint-21 kcal/mol
Surface area28650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.038, 67.721, 51.557
Angle α, β, γ (deg.)90.00, 103.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase / AtPPA-AT / Protein MATERNAL EFFECT EMBRYO ARREST 17


Mass: 51051.453 Da / Num. of mol.: 1 / Mutation: T84V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PAT, AAT, MEE17, At2g22250, T26C19.9 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9SIE1, aspartate transaminase, aspartate-prephenate aminotransferase, glutamate-prephenate aminotransferase
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 1.94 Å3/Da / Density % sol: 36.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 20% (w/v) PEG-6000, 100 mM citric acid, pH 5.0

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→30.68 Å / Num. obs: 25739 / % possible obs: 96.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.075 / Net I/av σ(I): 32.35 / Net I/σ(I): 32.35
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 5.56 / Num. unique obs: 1336 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data collection
SCALEPACKdata scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WMH

5wmh


Resolution: 2→30.68 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.23
RfactorNum. reflection% reflection
Rfree0.2151 1279 4.98 %
Rwork0.1666 --
obs0.1691 25706 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→30.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3049 0 10 147 3206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073115
X-RAY DIFFRACTIONf_angle_d1.0254224
X-RAY DIFFRACTIONf_dihedral_angle_d13.7511151
X-RAY DIFFRACTIONf_chiral_restr0.037493
X-RAY DIFFRACTIONf_plane_restr0.005541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9971-2.0770.30371310.23342711X-RAY DIFFRACTION97
2.077-2.17150.25541360.21462816X-RAY DIFFRACTION100
2.1715-2.2860.27721250.21532379X-RAY DIFFRACTION86
2.286-2.42920.24671660.18852780X-RAY DIFFRACTION100
2.4292-2.61660.26831360.18652815X-RAY DIFFRACTION100
2.6166-2.87980.23651450.19472797X-RAY DIFFRACTION100
2.8798-3.29610.22251610.17842815X-RAY DIFFRACTION100
3.2961-4.15110.19341420.15152550X-RAY DIFFRACTION91
4.1511-30.68340.1771370.13252764X-RAY DIFFRACTION95
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)
10.9154-0.52850.93630.881-1.61393.49040.3147-0.05010.7420.17190.13780.1258-0.44220.0978-0.43790.4772-0.11440.00150.37220.07220.65371.42776.802841.2668
22.6276-0.0871-0.95571.2220.71651.3477-0.0136-0.1207-0.0964-0.01240.04940.07950.01640.04270.00290.24430.0152-0.03630.2360.04440.2343-9.0715-10.529659.1506
32.4815-0.2426-0.18040.97570.14190.99050.1333-0.34040.51530.09740.0329-0.0693-0.32480.235-0.16970.4164-0.10420.0940.429-0.12030.47710.83679.652565.9778
41.6424-0.3672-0.65771.6707-0.10090.62750.15170.06810.0980.0122-0.0397-0.0185-0.1301-0.0862-0.11880.2801-0.01470.0370.27430.00150.3265-12.0015-4.878459.4603
53.25812.0957-1.22492.6274-1.89131.40410.223-0.5755-0.09310.0719-0.2884-0.195-0.03760.48290.05320.2408-0.0353-0.00970.4449-0.04120.332517.327-5.053459.7219
62.98271.2149-0.89064.9621-1.13033.42570.00750.18230.0802-0.5212-0.0433-0.25180.4150.16620.06460.3211-0.0478-0.00880.341-0.07050.279621.23292.981542.5913
72.26141.6523-0.44113.3482-1.69451.9185-0.06870.0857-0.1563-0.13990.0492-0.17340.13170.30090.1280.2026-0.04460.01590.3613-0.09150.319221.0977-2.166351.0614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 70 through 94 )
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 168 )
3X-RAY DIFFRACTION3chain 'A' and (resid 169 through 303 )
4X-RAY DIFFRACTION4chain 'A' and (resid 304 through 354 )
5X-RAY DIFFRACTION5chain 'A' and (resid 355 through 408 )
6X-RAY DIFFRACTION6chain 'A' and (resid 409 through 434 )
7X-RAY DIFFRACTION7chain 'A' and (resid 435 through 472 )

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