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- PDB-6dao: NahE WT selenomethionine -

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Basic information

Entry
Database: PDB / ID: 6dao
TitleNahE WT selenomethionine
ComponentsTrans-O-hydroxybenzylidenepyruvate hydratase-aldolase
KeywordsLYASE / aldolase / NahE
Function / homologytrans-o-hydroxybenzylidenepyruvate hydratase-aldolase / trans-o-hydroxybenzylidenepyruvate hydratase-aldolase activity / naphthalene catabolic process / aldehyde-lyase activity / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel / Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.939 Å
AuthorsMedellin, B.P. / LeVieux, J.A. / Zhang, Y.J. / Whitman, C.P.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-41239 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-104896 United States
Robert A. Welch FoundationF-1334 United States
Robert A. Welch FoundationF-1778 United States
CitationJournal: Biochemistry / Year: 2018
Title: Structural Characterization of the Hydratase-Aldolases, NahE and PhdJ: Implications for the Specificity, Catalysis, and N-Acetylneuraminate Lyase Subgroup of the Aldolase Superfamily.
Authors: LeVieux, J.A. / Medellin, B. / Johnson Jr., W.H. / Erwin, K. / Li, W. / Johnson, I.A. / Zhang, Y.J. / Whitman, C.P.
History
DepositionMay 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: 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 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
A: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase


Theoretical massNumber of molelcules
Total (without water)74,4792
Polymers74,4792
Non-polymers00
Water11,476637
1
B: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase

B: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase


Theoretical massNumber of molelcules
Total (without water)74,4792
Polymers74,4792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_677x-y+1,-y+2,-z+7/31
Buried area3980 Å2
ΔGint-25 kcal/mol
Surface area22600 Å2
MethodPISA
2
A: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase

A: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase


Theoretical massNumber of molelcules
Total (without water)74,4792
Polymers74,4792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_677x-y+1,-y+2,-z+7/31
Buried area4030 Å2
ΔGint-28 kcal/mol
Surface area23230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.310, 85.310, 133.313
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-690-

HOH

21A-699-

HOH

31A-711-

HOH

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Components

#1: Protein Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase / / THBPA hydratase-aldolase / 2'-hydroxybenzalpyruvate aldolase


Mass: 37239.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: nahE / Plasmid: pET
Details (production host): kanamycin and gentimicin resistant
Production host: Escherichia coli (E. coli) / Strain (production host): arctic express
References: UniProt: Q51947, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 35.57 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M 2-morpholin-4-ylethanesulfonic acid (MES) buffer (pH 6.5-8.0) and 21-26% PEG 2000 monomethyl ether (MME)
PH range: 6.5-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00, 1.5
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.51
ReflectionResolution: 1.939→40 Å / Num. obs: 42138 / % possible obs: 100 % / Redundancy: 2 % / Net I/σ(I): 15
Reflection shellResolution: 1.939→2.01 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementResolution: 1.939→38.08 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.77
RfactorNum. reflection% reflection
Rfree0.1851 4098 9.73 %
Rwork0.1455 --
obs0.1493 42138 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.939→38.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5053 0 0 637 5690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085177
X-RAY DIFFRACTIONf_angle_d0.8747044
X-RAY DIFFRACTIONf_dihedral_angle_d7.1133102
X-RAY DIFFRACTIONf_chiral_restr0.05777
X-RAY DIFFRACTIONf_plane_restr0.005908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9392-1.9620.22171160.16471292X-RAY DIFFRACTION99
1.962-1.98590.19561500.15671315X-RAY DIFFRACTION100
1.9859-2.01110.22071160.1471288X-RAY DIFFRACTION99
2.0111-2.03750.22171750.15071259X-RAY DIFFRACTION100
2.0375-2.06540.19961380.14451282X-RAY DIFFRACTION100
2.0654-2.0950.20521250.13991308X-RAY DIFFRACTION100
2.095-2.12620.21521470.14831287X-RAY DIFFRACTION100
2.1262-2.15940.18621320.15441293X-RAY DIFFRACTION100
2.1594-2.19480.19311520.14481290X-RAY DIFFRACTION100
2.1948-2.23270.19511190.1421325X-RAY DIFFRACTION100
2.2327-2.27330.20761250.14931295X-RAY DIFFRACTION100
2.2733-2.3170.20161540.14351296X-RAY DIFFRACTION100
2.317-2.36430.21921540.14621290X-RAY DIFFRACTION100
2.3643-2.41570.1951340.15051294X-RAY DIFFRACTION100
2.4157-2.47190.17851350.151315X-RAY DIFFRACTION100
2.4719-2.53370.20661660.15291268X-RAY DIFFRACTION100
2.5337-2.60220.2081340.15221319X-RAY DIFFRACTION100
2.6022-2.67870.19031500.15291305X-RAY DIFFRACTION100
2.6787-2.76520.16911820.15391264X-RAY DIFFRACTION100
2.7652-2.86390.22341540.14811294X-RAY DIFFRACTION100
2.8639-2.97860.20021310.16031327X-RAY DIFFRACTION100
2.9786-3.11410.18381380.14551316X-RAY DIFFRACTION100
3.1141-3.27820.18581250.14381354X-RAY DIFFRACTION100
3.2782-3.48340.15291180.14571329X-RAY DIFFRACTION100
3.4834-3.75220.18371320.13551350X-RAY DIFFRACTION100
3.7522-4.12940.151420.12131329X-RAY DIFFRACTION100
4.1294-4.72590.14061230.12271375X-RAY DIFFRACTION100
4.7259-5.95050.16291560.14841352X-RAY DIFFRACTION100
5.9505-38.08740.16661750.16261429X-RAY DIFFRACTION100

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