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- PDB-5wmk: Arabidopsis thaliana Prephenate Aminotransferase double mutant- T... -

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Basic information

Entry
Database: PDB / ID: 5wmk
TitleArabidopsis thaliana Prephenate Aminotransferase double mutant- T84V K169V
ComponentsBifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
KeywordsTRANSFERASE / 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
BORIC ACID / MALONATE ION / Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.398 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 29, 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)51,1853
Polymers51,0211
Non-polymers1642
Water8,539474
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)102,3716
Polymers102,0432
Non-polymers3284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6780 Å2
ΔGint-11 kcal/mol
Surface area28420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.498, 64.891, 51.933
Angle α, β, γ (deg.)90.00, 105.87, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-828-

HOH

21A-971-

HOH

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Components

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


Mass: 51021.402 Da / Num. of mol.: 1 / Mutation: T84V, K169V
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-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH3O3
#4: Water ChemComp-HOH / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 25% (w/v) PEG-1500, 100 mM MIB buffer (sodium malonate dibasic monohydrate, imidazole, boric 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: 1.4→28.02 Å / Num. obs: 73134 / % possible obs: 99.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 27.33
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.49 / Num. unique obs: 3572 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-3000data collection
PHASERphasing
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WMH

5wmh


Resolution: 1.398→28.015 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1776 3685 5.04 %
Rwork0.1606 --
obs0.1614 73128 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.398→28.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3055 0 11 474 3540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043221
X-RAY DIFFRACTIONf_angle_d0.8074393
X-RAY DIFFRACTIONf_dihedral_angle_d12.5191205
X-RAY DIFFRACTIONf_chiral_restr0.073514
X-RAY DIFFRACTIONf_plane_restr0.005568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3982-1.41660.31691250.27132384X-RAY DIFFRACTION89
1.4166-1.4360.25251470.24652617X-RAY DIFFRACTION99
1.436-1.45650.23751390.22382704X-RAY DIFFRACTION100
1.4565-1.47820.21951450.21552660X-RAY DIFFRACTION100
1.4782-1.50130.23031290.20522620X-RAY DIFFRACTION100
1.5013-1.52590.22731690.19392661X-RAY DIFFRACTION100
1.5259-1.55230.22851430.18882689X-RAY DIFFRACTION100
1.5523-1.58050.19581330.17442694X-RAY DIFFRACTION100
1.5805-1.61090.19931620.17732647X-RAY DIFFRACTION100
1.6109-1.64380.21681500.17362678X-RAY DIFFRACTION100
1.6438-1.67950.20841320.17162678X-RAY DIFFRACTION100
1.6795-1.71860.17961360.17352669X-RAY DIFFRACTION100
1.7186-1.76150.2111520.17082703X-RAY DIFFRACTION100
1.7615-1.80910.17821340.16352662X-RAY DIFFRACTION100
1.8091-1.86240.17151410.16762673X-RAY DIFFRACTION100
1.8624-1.92250.17391330.1672711X-RAY DIFFRACTION100
1.9225-1.99120.17211600.15782644X-RAY DIFFRACTION100
1.9912-2.07090.18631220.15822709X-RAY DIFFRACTION100
2.0709-2.16510.16981560.15392686X-RAY DIFFRACTION100
2.1651-2.27920.18131480.15612653X-RAY DIFFRACTION100
2.2792-2.42190.22111180.15572716X-RAY DIFFRACTION100
2.4219-2.60880.15641420.15752709X-RAY DIFFRACTION100
2.6088-2.87110.16951120.16242719X-RAY DIFFRACTION100
2.8711-3.2860.17191480.15292692X-RAY DIFFRACTION100
3.286-4.13780.15121510.14022720X-RAY DIFFRACTION100
4.1378-28.02060.16141580.15052745X-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)
15.7422-5.40740.11646.9015-0.8960.64340.08210.0907-0.0397-0.34730.02280.18810.1036-0.0908-0.0480.1511-0.0402-0.02720.1434-0.00370.121914.73944.8903-7.4682
23.9130.3954-0.52940.67580.02780.2812-0.05590.0177-0.3002-0.08610.0246-0.0351-0.0171-0.02020.04370.1727-0.0022-0.00630.1471-0.00940.1165.1173-14.79642.8011
30.97940.01130.15880.4798-0.17690.4781-0.0396-0.04420.08390.01120.0119-0.0328-0.0440.00310.03170.11810.00580.00710.1267-0.02060.10719.58797.102414.3953
41.0496-0.3829-0.01290.78440.14010.442-0.0068-0.07540.01480.00770.0264-0.0063-0.02810.0015-0.01560.1362-0.0050.01580.15340.00950.12626.61623.3217.6752
53.76860.6260.20760.84140.240.82540.0343-0.117-0.16450.0355-0.0213-0.07030.01790.06590.00440.11150.0208-0.00220.0683-0.00030.08514.7653-12.621912.5391
60.91170.6629-0.29661.6733-0.54620.4978-0.0279-0.0276-0.0593-0.1321-0.0126-0.26750.04590.06470.04760.1153-0.00640.02710.144-0.0220.182333.26220.21131.5845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 71 through 96 )
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 138 )
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 251 )
4X-RAY DIFFRACTION4chain 'A' and (resid 252 through 335 )
5X-RAY DIFFRACTION5chain 'A' and (resid 336 through 380 )
6X-RAY DIFFRACTION6chain 'A' and (resid 381 through 473 )

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