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- PDB-5whx: PREPHENATE DEHYDROGENASE FROM SOYBEAN -

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Basic information

Entry
Database: PDB / ID: 5whx
TitlePREPHENATE DEHYDROGENASE FROM SOYBEAN
ComponentsPrephenate dehydrogenase 1
KeywordsOXIDOREDUCTASE / TYROSINE BIOSYNTHESIS
Function / homology
Function and homology information


prephenate dehydrogenase (NADP+) / arogenate dehydrogenase (NADP+) activity / prephenate dehydrogenase (NADP+) activity / prephenate dehydrogenase (NAD+) activity / tyrosine biosynthetic process / NAD+ binding
Similarity search - Function
Arogenate dehydrogenase 1/2 / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate dehydrogenase / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate/arogenate dehydrogenase domain profile. / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
CITRIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Prephenate dehydrogenase 1
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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: Nat. Chem. Biol. / Year: 2017
Title: Molecular basis of the evolution of alternative tyrosine biosynthetic routes in plants.
Authors: Schenck, C.A. / Holland, C.K. / Schneider, M.R. / Men, Y. / Lee, S.G. / Jez, J.M. / Maeda, H.A.
History
DepositionJul 18, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionAug 2, 2017ID: 5T8X
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Refinement description / Category: citation / software
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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: Prephenate dehydrogenase 1
B: Prephenate dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2366
Polymers61,3642
Non-polymers1,8714
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-60 kcal/mol
Surface area20410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.002, 55.275, 67.942
Angle α, β, γ (deg.)107.44, 98.91, 103.23
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Prephenate dehydrogenase 1


Mass: 30682.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: LOC100787362, PDH1, GLYMA_18G023100 / Plasmid: PET28A / Cell line (production host): ROSETTA 2 / Production host: Escherichia coli (E. coli)
References: UniProt: I1MYY4, prephenate dehydrogenase (NADP+)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 20% PEG-4000 AND 100 MM SODIUM CITRATE, PH 5.5 WITH 30% (W/V) D-SORBITOL AS AN ADDITIVE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 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: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.69→32.41 Å / Num. obs: 64687 / % possible obs: 97 % / Redundancy: 1.96 % / Rmerge(I) obs: 0.057 / Rsym value: 0.04 / Net I/σ(I): 13.77
Reflection shellResolution: 1.69→1.72 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3130 / % possible all: 94.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASERphasing
PHENIX1.9_1692refinement
HKL-3000data collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T9E

5t9e


Resolution: 1.69→32.41 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 18.37
RfactorNum. reflection% reflection
Rfree0.182 3163 4.97 %
Rwork0.153 --
obs0.155 63602 94.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.69→32.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3997 0 122 516 4635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074338
X-RAY DIFFRACTIONf_angle_d1.1715902
X-RAY DIFFRACTIONf_dihedral_angle_d13.751634
X-RAY DIFFRACTIONf_chiral_restr0.042678
X-RAY DIFFRACTIONf_plane_restr0.005743
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6931-1.71830.26011060.21492128X-RAY DIFFRACTION76
1.7183-1.74520.23271290.21572574X-RAY DIFFRACTION93
1.7452-1.77380.23861450.2062583X-RAY DIFFRACTION93
1.7738-1.80440.21821610.20672528X-RAY DIFFRACTION93
1.8044-1.83720.24411190.19662665X-RAY DIFFRACTION93
1.8372-1.87250.23581330.18372535X-RAY DIFFRACTION94
1.8725-1.91070.23241520.18372635X-RAY DIFFRACTION95
1.9107-1.95230.24111300.17592651X-RAY DIFFRACTION95
1.9523-1.99770.23321360.17312665X-RAY DIFFRACTION95
1.9977-2.04760.2131390.16682628X-RAY DIFFRACTION95
2.0476-2.1030.20641270.162635X-RAY DIFFRACTION95
2.103-2.16490.16851330.15952671X-RAY DIFFRACTION96
2.1649-2.23470.20241370.15182663X-RAY DIFFRACTION96
2.2347-2.31460.16331380.14822681X-RAY DIFFRACTION96
2.3146-2.40720.18031270.15162678X-RAY DIFFRACTION96
2.4072-2.51670.18021360.1482700X-RAY DIFFRACTION97
2.5167-2.64940.16641590.15582649X-RAY DIFFRACTION97
2.6494-2.81530.20531290.16062694X-RAY DIFFRACTION97
2.8153-3.03250.18281550.1542704X-RAY DIFFRACTION97
3.0325-3.33740.15411410.14032677X-RAY DIFFRACTION97
3.3374-3.81970.16011340.13032711X-RAY DIFFRACTION97
3.8197-4.80980.14181420.12182677X-RAY DIFFRACTION97
4.8098-32.41140.16971550.15362707X-RAY DIFFRACTION98
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)
11.74220.22680.48510.89810.36931.6932-0.02960.14770.0533-0.06290.0254-0.0546-0.10010.08460.01120.10680.00690.00480.12240.00610.12171.806-44.5786-33.0478
20.1129-0.0552-0.03963.0637-2.43543.1831-0.00420.02350.01210.0741-0.0671-0.1254-0.00250.05680.09270.10010.01920.00370.132-0.03480.1338-16.1968-55.7053-14.5757
31.0848-0.02790.23682.22220.73721.47270.009-0.0901-0.09210.2619-0.0086-0.01430.1587-0.03710.00820.14580.00580.00910.11570.01770.118315.0795-33.07041.8817
41.00150.7321-0.84211.4756-1.44122.5662-0.13860.0367-0.1213-0.01470.06310.00720.2067-0.05010.080.11940.0151-0.02560.165-0.01420.177712.8266-8.2261-13.0258
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 8 THROUGH 183 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 184 THROUGH 257 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 8 THROUGH 183 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 184 THROUGH 260 )

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