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- PDB-5wmh: Arabidopsis thaliana prephenate aminotransferase -

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Basic information

Entry
Database: PDB / ID: 5wmh
TitleArabidopsis thaliana prephenate aminotransferase
ComponentsBifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
KeywordsTRANSFERASE / 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
PYRIDOXAL-5'-PHOSPHATE / Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHolland, C.K. / Jez, J.M.
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: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_validate_close_contact / struct_conn
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
B: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
C: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
D: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
E: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
F: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,80312
Polymers306,3216
Non-polymers1,4836
Water73941
1
A: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
B: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6014
Polymers102,1072
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-21 kcal/mol
Surface area28670 Å2
MethodPISA
2
C: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
D: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6014
Polymers102,1072
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-22 kcal/mol
Surface area28620 Å2
MethodPISA
3
E: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
F: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6014
Polymers102,1072
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-26 kcal/mol
Surface area29740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.343, 111.575, 141.775
Angle α, β, γ (deg.)90.00, 90.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 51053.426 Da / Num. of mol.: 6
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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.07 Å3/Da / Density % sol: 40.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG-3350 and 200 mM magnesium formate

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.988 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.96→33.27 Å / Num. obs: 51962 / % possible obs: 99.8 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.43
Reflection shellResolution: 2.96→3.05 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 7.8 / Num. unique obs: 4284 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-3000data collection
PHASERphasing
SCALEPACKdata scaling
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J32

1j32


Resolution: 3→33.268 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2704 2515 5.02 %
Rwork0.2097 --
obs0.2128 50103 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→33.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18161 0 90 41 18292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01518607
X-RAY DIFFRACTIONf_angle_d1.92525262
X-RAY DIFFRACTIONf_dihedral_angle_d3.79212009
X-RAY DIFFRACTIONf_chiral_restr0.0882932
X-RAY DIFFRACTIONf_plane_restr0.0153225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.05770.35181410.27282621X-RAY DIFFRACTION100
3.0577-3.120.3341250.27462642X-RAY DIFFRACTION100
3.12-3.18780.33251550.27432651X-RAY DIFFRACTION100
3.1878-3.26190.37691360.27132608X-RAY DIFFRACTION100
3.2619-3.34340.28091420.26292664X-RAY DIFFRACTION100
3.3434-3.43370.34781460.25112611X-RAY DIFFRACTION100
3.4337-3.53470.29761380.24112652X-RAY DIFFRACTION100
3.5347-3.64860.28951490.24072618X-RAY DIFFRACTION100
3.6486-3.77890.25921400.24282618X-RAY DIFFRACTION100
3.7789-3.92990.30321290.21342650X-RAY DIFFRACTION100
3.9299-4.10850.28321360.20072646X-RAY DIFFRACTION100
4.1085-4.32470.26011460.18692640X-RAY DIFFRACTION100
4.3247-4.5950.24361500.17352635X-RAY DIFFRACTION100
4.595-4.94870.25771420.17162651X-RAY DIFFRACTION100
4.9487-5.44470.24021270.18042677X-RAY DIFFRACTION100
5.4447-6.22810.24821350.2022667X-RAY DIFFRACTION100
6.2281-7.82990.21861260.20482690X-RAY DIFFRACTION100
7.8299-33.26980.23421520.17972647X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -16.6955 Å / Origin y: -12.5568 Å / Origin z: 37.016 Å
111213212223313233
T0.5531 Å2-0.0751 Å20.0203 Å2-0.5311 Å2-0.0138 Å2--0.4608 Å2
L0.3058 °20.3733 °2-0.0916 °2-0.7889 °2-0.2861 °2---0.0802 °2
S0.0465 Å °-0.0648 Å °0.1004 Å °0.2024 Å °0.0169 Å °0.1135 Å °-0.057 Å °-0.048 Å °-0.0665 Å °
Refinement TLS groupSelection details: all

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