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- PDB-5xtg: Crystal structure of the cis-dihydrodiol naphthalene dehydrogenas... -

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Basic information

Entry
Database: PDB / ID: 5xtg
TitleCrystal structure of the cis-dihydrodiol naphthalene dehydrogenase NahB from Pseudomonas sp. MC1 in the presence of NAD+ and 2,3-dihydroxybiphenyl
Components2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase
KeywordsOXIDOREDUCTASE / tetramer / cis-dihydrodiol naphthalene dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / nucleotide binding
Similarity search - Function
: / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BIPHENYL-2,3-DIOL / CITRIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase
Similarity search - Component
Biological speciesPseudomonas sp. MC1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.318 Å
AuthorsPark, A.K. / Kim, H.-W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Korea Polar Research InstitutePE17080 Korea, Republic Of
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structure of cis-dihydrodiol naphthalene dehydrogenase (NahB) from Pseudomonas sp. MC1: Insights into the early binding process of the substrate
Authors: Park, A.K. / Kim, H. / Kim, I.S. / Roh, S.J. / Shin, S.C. / Lee, J.H. / Park, H. / Kim, H.W.
History
DepositionJun 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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
B: 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8634
Polymers29,8211
Non-polymers1,0423
Water61334
1
B: 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase
hetero molecules

B: 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase
hetero molecules

B: 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase
hetero molecules

B: 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,45216
Polymers119,2854
Non-polymers4,16712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area20460 Å2
ΔGint-162 kcal/mol
Surface area30880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.082, 70.082, 119.181
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase


Mass: 29821.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. MC1 (bacteria) / Gene: nahB, pYIC1_37 / Production host: Escherichia coli (E. coli) / References: UniProt: G9G7I7
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-BPY / BIPHENYL-2,3-DIOL


Mass: 186.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: ammonium citrate tribasic, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 13507 / % possible obs: 97.7 % / Redundancy: 22.6 % / Biso Wilson estimate: 44.53 Å2 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.033 / Rrim(I) all: 0.156 / Χ2: 2.681 / Net I/σ(I): 11 / Num. measured all: 305059
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.3415.31.0274110.9190.2491.0591.47860.4
2.34-2.3819.60.9886590.9720.2161.0121.5100
2.38-2.4320.91.066810.9690.2281.0841.44100
2.43-2.4822.10.926620.9810.1940.9411.511100
2.48-2.5323.50.826640.9840.170.8381.567100
2.53-2.5924.60.796860.9860.1610.8071.663100
2.59-2.6625.60.76780.9930.140.7151.64100
2.66-2.7325.90.6116640.9910.1220.6231.782100
2.73-2.8126.10.5386900.9930.1070.5481.86100
2.81-2.926.20.4016790.9960.080.4091.951100
2.9-3260.336860.9960.0660.3372.127100
3-3.1225.60.2446740.9980.0490.2492.489100
3.12-3.2625.40.2076830.9960.0420.2122.846100
3.26-3.4424.70.1526990.9990.0310.1553.226100
3.44-3.6521.70.1316940.9980.0290.1353.91100
3.65-3.9320.50.1046970.9980.0240.1074.44599.9
3.93-4.3320.50.0826960.9990.0190.0854.68699.3
4.33-4.95190.0727100.9970.0170.0745.08898.9
4.95-6.2419.30.0697250.9980.0160.0714.63999.7
6.24-5017.30.067690.9990.0140.0614.44595.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y93

2y93


Resolution: 2.318→30.206 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2228 662 4.94 %
Rwork0.1743 12744 -
obs0.1767 13406 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.93 Å2 / Biso mean: 58.1046 Å2 / Biso min: 30.33 Å2
Refinement stepCycle: final / Resolution: 2.318→30.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 102 34 1876
Biso mean--82.07 51.79 -
Num. residues----233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121843
X-RAY DIFFRACTIONf_angle_d1.3332499
X-RAY DIFFRACTIONf_chiral_restr0.058286
X-RAY DIFFRACTIONf_plane_restr0.007313
X-RAY DIFFRACTIONf_dihedral_angle_d17.6971078
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3175-2.49640.29031350.21172492262799
2.4964-2.74750.24821190.20225102629100
2.7475-3.14470.29821240.20325372661100
3.1447-3.96060.221320.18482537266999
3.9606-30.20830.19151520.14922668282098

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