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- PDB-5wml: Arabidopsis thaliana Prephenate Aminotransferase mutant- K306A -

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Basic information

Entry
Database: PDB / ID: 5wml
TitleArabidopsis thaliana Prephenate Aminotransferase mutant- K306A
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
GLUTAMIC ACID / 4'-DEOXY-4'-AMINOPYRIDOXAL-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: 2.103 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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,7816
Polymers101,9912
Non-polymers7914
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-32 kcal/mol
Surface area27890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.813, 60.117, 66.734
Angle α, β, γ (deg.)74.78, 76.70, 83.92
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 50995.324 Da / Num. of mol.: 2 / Mutation: K306A
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-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 1.91 Å3/Da / Density % sol: 35.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 25% (w/v) PEG-1500, 100 mM MIB buffer, 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: Mar 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.103→39.43 Å / Num. obs: 39241 / % possible obs: 90 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 11.38
Reflection shellResolution: 2.103→2.14 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 1947 / % possible all: 86.3

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Processing

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

5wmh


Resolution: 2.103→39.426 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.24
RfactorNum. reflection% reflection
Rfree0.212 2000 5.1 %
Rwork0.1531 --
obs0.1562 39236 89.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.103→39.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6107 0 50 432 6589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076285
X-RAY DIFFRACTIONf_angle_d1.158534
X-RAY DIFFRACTIONf_dihedral_angle_d14.6022314
X-RAY DIFFRACTIONf_chiral_restr0.043993
X-RAY DIFFRACTIONf_plane_restr0.0051094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1031-2.15570.27281250.19362341X-RAY DIFFRACTION78
2.1557-2.2140.24871390.17652577X-RAY DIFFRACTION87
2.214-2.27920.23191400.17512593X-RAY DIFFRACTION87
2.2792-2.35270.25621330.17322489X-RAY DIFFRACTION84
2.3527-2.43680.24861390.17852584X-RAY DIFFRACTION87
2.4368-2.53430.25611500.17252780X-RAY DIFFRACTION94
2.5343-2.64970.25631490.17232799X-RAY DIFFRACTION94
2.6497-2.78930.22671500.17252794X-RAY DIFFRACTION94
2.7893-2.9640.24611460.17432720X-RAY DIFFRACTION91
2.964-3.19280.26891440.17192670X-RAY DIFFRACTION90
3.1928-3.51390.21951380.14932568X-RAY DIFFRACTION86
3.5139-4.0220.1741520.13642823X-RAY DIFFRACTION95
4.022-5.06560.16931490.12012790X-RAY DIFFRACTION94
5.0656-39.43290.15961460.13242708X-RAY DIFFRACTION91
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)
10.2143-0.1995-0.00390.19580.02270.0093-0.08310.0633-0.0169-0.1250.06660.08670.04780.0366-00.20340.0154-0.02080.20070.00550.1314-10.6438-3.5182-11.7398
20.3071-0.0909-0.11540.3985-0.00840.04740.04990.0425-0.03210.1325-0.0013-0.00190.18050.064900.1486-0.00120.00610.15230.01520.14291.6168-14.09526.1505
30.63550.1758-0.31270.46360.22860.4934-0.0143-0.0772-0.00530.00840.0439-0.0901-0.02610.010800.06880.01620.00360.127-0.01030.104414.7398-2.2147-4.8875
40.31810.14590.04450.3374-0.13660.6070.02760.0629-0.0389-0.12680.0171-0.0375-0.0961-0.1343-00.1417-0.0120.02360.2265-0.00280.12999.1119-2.7734-23.1932
50.2840.34220.11920.37290.13970.2515-0.06660.1502-0.0833-0.11540.0795-0.04220.03690.066300.13520.00820.03530.1434-0.0230.188717.1938-10.1186-17.0317
60.0180.0297-0.03870.24970.33090.47960.0068-0.0763-0.0606-0.08020.044-0.10890.04990.070800.13140.0229-0.00610.17670.01040.130614.9678-6.6925-6.0498
70.05270.0123-0.14640.0702-0.16530.42080.11820.0470.01310.1768-0.0686-0.018-0.02690.10070.00010.1316-0.0021-0.00840.15030.01860.149410.9479-1.29783.1988
80.2237-0.2186-0.12550.2460.13360.06750.09350.1218-0.10.0746-0.0781-0.05950.30980.09750.00020.21320.0276-0.01030.1381-0.03070.19098.1882-28.0585-9.803
90.30240.08190.18850.4279-0.24480.33060.02710.0976-0.0454-0.2860.06370.05680.1721-0.01060.00210.2114-0.0115-0.03630.1511-0.01420.1377-5.9159-19.8304-23.148
100.3677-0.1095-0.20980.08830.21680.5544-0.10430.0972-0.4928-0.2361-0.00730.0920.63280.0639-0.01640.2876-0.0431-0.06720.2005-0.00960.2827-8.7725-29.2056-22.7713
110.0291-0.0411-0.0950.01360.08260.202-0.1044-0.20120.04130.17110.18930.112-0.1255-0.26590.00040.30820.04220.02040.22290.0020.224812.214212.10935.1004
120.4363-0.15510.01750.26510.3370.30630.0252-0.0091-0.02070.1199-0.05340.09160.0803-0.07480.00430.0859-0.00370.00750.0710.01280.0682-7.6747-3.679611.0279
130.82330.1084-0.02630.53780.44630.7762-0.00090.00990.0895-0.0046-0.02310.0194-0.0918-0.043400.14530.00890.01050.14150.01050.172-11.466718.7615.1149
140.1053-0.26780.03140.5761-0.00990.16620.05680.00310.00350.0316-0.08930.00490.04520.0546-00.1139-0.02780.00270.10770.01220.1195-8.3102-1.43194.9932
150.2368-0.2118-0.14010.20210.13870.0754-0.0016-0.06290.13720.3555-0.00360.16750.227-0.0115-0.00010.25880.01080.03820.2094-0.00030.1692-6.368910.213628.5396
160.05770.0159-0.06930.31670.05150.04240.1042-0.10550.08880.1652-0.1496-0.0103-0.00190.084-0.00010.2023-0.0237-0.00760.206-0.02750.213.119825.806823.0251
170.396-0.06620.04560.44150.34980.3641-0.067-0.19720.06210.04410.0138-0.26540.00650.21110.00010.16990.0123-0.04660.23790.00640.208911.177422.138622.5443
180.09830.13890.22930.43720.28340.5391-0.1025-0.2202-0.04550.0685-0.0605-0.11010.0368-0.0012-0.12680.40680.04690.10510.6187-0.28730.71021.07250.07780.7277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 70:96 )A70 - 96
2X-RAY DIFFRACTION2( CHAIN A AND RESID 97:138 )A97 - 138
3X-RAY DIFFRACTION3( CHAIN A AND RESID 139:190 )A139 - 190
4X-RAY DIFFRACTION4( CHAIN A AND RESID 191:239 )A191 - 239
5X-RAY DIFFRACTION5( CHAIN A AND RESID 240:287 )A240 - 287
6X-RAY DIFFRACTION6( CHAIN A AND RESID 288:321 )A288 - 321
7X-RAY DIFFRACTION7( CHAIN A AND RESID 322:354 )A322 - 354
8X-RAY DIFFRACTION8( CHAIN A AND RESID 355:380 )A355 - 380
9X-RAY DIFFRACTION9( CHAIN A AND RESID 381:451 )A381 - 451
10X-RAY DIFFRACTION10( CHAIN A AND RESID 452:473 )A452 - 473
11X-RAY DIFFRACTION11( CHAIN B AND RESID 71:96 )B71 - 96
12X-RAY DIFFRACTION12( CHAIN B AND RESID 97:167 )B97 - 167
13X-RAY DIFFRACTION13( CHAIN B AND RESID 168:303 )B168 - 303
14X-RAY DIFFRACTION14( CHAIN B AND RESID 304:354 )B304 - 354
15X-RAY DIFFRACTION15( CHAIN B AND RESID 355:380 )B355 - 380
16X-RAY DIFFRACTION16( CHAIN B AND RESID 381:408 )B381 - 408
17X-RAY DIFFRACTION17( CHAIN B AND RESID 409:472 )B409 - 472
18X-RAY DIFFRACTION18( CHAIN A AND RESID 502:502 ) OR ( CHAIN B AND RESID 502:502 )A502
19X-RAY DIFFRACTION18( CHAIN A AND RESID 502:502 ) OR ( CHAIN B AND RESID 502:502 )B502

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