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

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Basic information

Entry
Database: PDB / ID: 5xtf
TitleCrystal structure of the cis-dihydrodiol naphthalene dehydrogenase NahB from Pseudomonas sp. MC1
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
2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase
Similarity search - Component
Biological speciesPseudomonas sp. MC1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.095 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

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Assembly

Deposited unit
A: 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase
B: 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)59,6422
Polymers59,6422
Non-polymers00
Water2,918162
1
A: 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase
B: 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase

A: 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase
B: 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)119,2854
Polymers119,2854
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575x,-y+2,-z1
Buried area12770 Å2
ΔGint-105 kcal/mol
Surface area30970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.162, 69.695, 117.692
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 29821.234 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.36 Å3/Da / Density % sol: 43.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Tris-Cl, CaCl2, PEG6000

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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: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.095→50 Å / Num. obs: 29534 / % possible obs: 94.5 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.04 / Rrim(I) all: 0.115 / Χ2: 1.379 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1430.3040.80.1750.3550.49273.9
2.14-2.183.10.2860.7850.1540.3280.51179.7
2.18-2.223.30.2690.8550.1450.3080.585.1
2.22-2.263.40.2680.8550.1420.3060.54889.2
2.26-2.313.60.2590.9050.1360.2960.56592
2.31-2.374.20.2620.8650.1280.2940.58195
2.37-2.424.80.2560.8940.1170.2830.59796.8
2.42-2.4950.240.9290.1070.2640.5997.2
2.49-2.565.20.2280.9480.0990.2490.70496.7
2.56-2.655.40.2040.9630.0860.2230.71497.7
2.65-2.745.50.1890.980.0770.2050.90897.9
2.74-2.855.60.1710.9770.0690.1850.97197.5
2.85-2.986.80.1510.9890.0550.1621.08698.4
2.98-3.147.20.13610.080.1621.37298.7
3.14-3.337.80.1210.9950.0410.1281.54998.9
3.33-3.598.10.1050.9960.0350.1111.88699
3.59-3.958.40.0950.9960.0320.1011.98599.2
3.95-4.529.60.0870.9950.0280.0912.1499.4
4.52-5.79.10.0850.9970.0270.0892.05498.6
5.7-109.50.0780.9960.0250.0822.02297.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

2y93


Resolution: 2.095→44.963 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 26.82
RfactorNum. reflection% reflection
Rfree0.2437 1493 5.07 %
Rwork0.2043 --
obs0.2063 29429 94.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.77 Å2 / Biso mean: 31.4648 Å2 / Biso min: 12.19 Å2
Refinement stepCycle: final / Resolution: 2.095→44.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3414 0 0 162 3576
Biso mean---37.83 -
Num. residues----457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093470
X-RAY DIFFRACTIONf_angle_d0.9674693
X-RAY DIFFRACTIONf_chiral_restr0.054546
X-RAY DIFFRACTIONf_plane_restr0.005601
X-RAY DIFFRACTIONf_dihedral_angle_d15.5312063
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0954-2.16310.35791170.29261945206274
2.1631-2.24040.29861150.27032306242186
2.2404-2.33010.32091220.25462457257992
2.3301-2.43610.28951190.24172583270296
2.4361-2.56450.26761550.22892568272397
2.5645-2.72520.23091280.21762631275998
2.7252-2.93560.28281450.20832607275298
2.9356-3.23090.23431360.2032661279799
3.2309-3.69820.24461410.18392706284799
3.6982-4.65860.19251750.16242677285299
4.6586-44.97280.20731400.18372795293597

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