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- PDB-5t9f: Prephenate Dehydrogenase N222D mutant from Soybean -

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Basic information

Entry
Database: PDB / ID: 5t9f
TitlePrephenate Dehydrogenase N222D mutant from Soybean
ComponentsPrephenate dehydrogenase 1
KeywordsOXIDOREDUCTASE / dehydrogenase / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / TYROSINE / Prephenate dehydrogenase 1
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.994 Å
AuthorsHolland, C.K. / Jez, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-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
DepositionSep 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)63,2166
Polymers61,3662
Non-polymers1,8494
Water7,837435
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-9 kcal/mol
Surface area24820 Å2
2
A: Prephenate dehydrogenase 1
hetero molecules

B: Prephenate dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2166
Polymers61,3662
Non-polymers1,8494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
Buried area7350 Å2
ΔGint-59 kcal/mol
Surface area20640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.445, 55.046, 68.387
Angle α, β, γ (deg.)107.82, 99.56, 102.58
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Prephenate dehydrogenase 1 / / Uncharacterized protein


Mass: 30683.205 Da / Num. of mol.: 2 / Mutation: N222D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: 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 / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 2 mM of an oxometalates solution containing 0.005 M sodium chromate tetrahydrate, 0.005 M sodium molybdate dihydrate, 0.005M sodium tungstate dihydrate, and 0.005 M sodium orthovanadate, 0.1 ...Details: 2 mM of an oxometalates solution containing 0.005 M sodium chromate tetrahydrate, 0.005 M sodium molybdate dihydrate, 0.005M sodium tungstate dihydrate, and 0.005 M sodium orthovanadate, 0.1 M of MOPSO and Bis-Tris, pH 6.5, and 50% v/v of a precipitant mixture of 20% w/v PEG 8000 and 40% v/v 1,5-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.994→33.85 Å / Num. obs: 36694 / % possible obs: 88.9 % / Redundancy: 1.7 % / Net I/σ(I): 10.19
Reflection shellResolution: 1.994→2.048 Å / % possible all: 85.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data collection
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 1.994→33.846 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 20.18
RfactorNum. reflection% reflection
Rfree0.2058 1832 4.99 %
Rwork0.1579 --
obs0.1602 36686 88.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.994→33.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3988 0 122 435 4545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084266
X-RAY DIFFRACTIONf_angle_d0.9125783
X-RAY DIFFRACTIONf_dihedral_angle_d14.3332535
X-RAY DIFFRACTIONf_chiral_restr0.054664
X-RAY DIFFRACTIONf_plane_restr0.005723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9943-2.04820.26451240.19552420X-RAY DIFFRACTION80
2.0482-2.10840.24771400.18032632X-RAY DIFFRACTION86
2.1084-2.17650.22251300.18562558X-RAY DIFFRACTION85
2.1765-2.25420.24321410.18872565X-RAY DIFFRACTION85
2.2542-2.34450.24441290.18552493X-RAY DIFFRACTION81
2.3445-2.45120.25471410.17052775X-RAY DIFFRACTION91
2.4512-2.58030.20281530.16992758X-RAY DIFFRACTION92
2.5803-2.74190.20621310.16672801X-RAY DIFFRACTION91
2.7419-2.95350.21151460.16222703X-RAY DIFFRACTION90
2.9535-3.25050.21371510.16152751X-RAY DIFFRACTION91
3.2505-3.72040.2041510.15042832X-RAY DIFFRACTION94
3.7204-4.68530.1711410.1292743X-RAY DIFFRACTION90
4.6853-33.85050.1851540.14842823X-RAY DIFFRACTION93
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)
12.01930.28210.82490.89920.59622.13510.00160.1208-0.0473-0.08570.0201-0.0503-0.04960.0813-0.02390.18910.00160.01930.18440.00420.20571.6191-44.4711-32.7838
20.19150.5342-0.47273.2992-1.99122.62-0.02720.02240.02940.1331-0.0429-0.1352-0.03360.14710.07940.13990.01340.00020.1791-0.01480.1838-16.9193-55.8393-14.5677
32.7377-1.2163-0.50063.76820.42832.79940.0348-0.109-0.0428-0.0047-0.0107-0.2020.10910.0499-0.00190.1868-0.00650.02280.1664-0.00260.23515.7009-40.2653-5.9646
41.9809-0.1034-0.774.96830.86052.1359-0.03910.0152-0.25360.3487-0.10720.21360.2596-0.21810.1010.2456-0.03040.02640.24910.01040.29047.3209-39.05430.6434
53.03270.99110.02262.8571-0.4283.5762-0.0478-0.1984-0.23170.52560.06040.32960.2834-0.35540.0020.3551-0.01150.07530.2691-0.01280.22248.577-31.83498.2085
62.1089-0.30770.63034.01340.36671.5062-0.0101-0.0585-0.05360.3672-0.0038-0.47630.01530.11420.01490.2083-0.0006-0.040.1946-0.00740.223321.2485-27.24154.1938
74.10970.656-0.23542.7759-0.69363.1096-0.0470.5432-0.145-0.3147-0.02150.03030.30190.06640.13420.2524-0.00030.02050.2417-0.03780.271715.2379-10.8176-18.833
81.60831.8761-2.79343.3517-4.54486.3291-0.44140.0614-0.549-0.44330.0972-0.75380.64430.30950.36420.34150.05060.01150.2265-0.03440.310519.5124-15.0534-19.3099
91.7385-0.0543-0.09283.48482.00144.61790.1123-0.0917-0.15720.0339-0.12530.40790.1101-0.2696-0.0380.1640.02460.00060.18050.02510.25467.2953-17.4036-3.797
103.09030.6173-0.75583.224-4.89237.80620.1130.07460.18750.47160.03690.2158-0.5648-0.0699-0.25440.22820.0537-0.01760.1946-0.05630.239111.87834.3617-9.747
111.99992.00022.00011.99981.99972.00040.33020.1287-0.6834-0.55760.02720.99120.59250.1507-0.32850.67670.01530.1830.64610.17110.7675-4.3078-53.1663-22.5092
122.13831.76951.6842.5581.78012.5690.0429-0.36010.20840.08520.0197-0.08980.11861.0539-0.09740.7780.23350.02360.52090.0090.739617.519-22.7315-8.456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:183 )A9 - 183
2X-RAY DIFFRACTION2( CHAIN A AND RESID 184:257 )A184 - 257
3X-RAY DIFFRACTION3( CHAIN B AND RESID 8:50 )B8 - 50
4X-RAY DIFFRACTION4( CHAIN B AND RESID 51:83 )B51 - 83
5X-RAY DIFFRACTION5( CHAIN B AND RESID 84:113 )B84 - 113
6X-RAY DIFFRACTION6( CHAIN B AND RESID 114:183 )B114 - 183
7X-RAY DIFFRACTION7( CHAIN B AND RESID 184:206 )B184 - 206
8X-RAY DIFFRACTION8( CHAIN B AND RESID 207:221 )B207 - 221
9X-RAY DIFFRACTION9( CHAIN B AND RESID 222:236 )B222 - 236
10X-RAY DIFFRACTION10( CHAIN B AND RESID 237:260 )B237 - 260
11X-RAY DIFFRACTION11( CHAIN A AND RESID 302:302 )A302
12X-RAY DIFFRACTION12( CHAIN B AND RESID 302:302 )B302

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