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- PDB-5zxu: Crystal structure of CurA in complex with NADPH from Vibrio vulnificus -

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Basic information

Entry
Database: PDB / ID: 5zxu
TitleCrystal structure of CurA in complex with NADPH from Vibrio vulnificus
ComponentsNADP-dependent oxidoreductase
KeywordsOXIDOREDUCTASE / Reductase
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Oxidoreductase, N-terminal domain / N-terminal domain of oxidoreductase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain ...Oxidoreductase, N-terminal domain / N-terminal domain of oxidoreductase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / NADP-dependent oxidoreductase
Similarity search - Component
Biological speciesVibrio vulnificus MO6-24/O (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKim, M.-K. / Bae, D.-W. / Cha, S.-S.
CitationJournal: J. Agric. Food Chem. / Year: 2018
Title: Structural and Biochemical Characterization of the Curcumin-Reducing Activity of CurA from Vibrio vulnificus.
Authors: Park, S.B. / Bae, D.W. / Clavio, N.A.B. / Zhao, L. / Jeong, C.S. / Choi, B.M. / Macalino, S.J.Y. / Cha, H.J. / Park, J.B. / Lee, J.H. / Nam, S.J. / Choi, S. / Kim, M.K. / Cha, S.S.
History
DepositionMay 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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: NADP-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1852
Polymers36,4401
Non-polymers7451
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-7 kcal/mol
Surface area14930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.137, 90.137, 105.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein NADP-dependent oxidoreductase


Mass: 36439.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: WP_015728066 / Source: (gene. exp.) Vibrio vulnificus MO6-24/O (bacteria) / Strain: MO6-24/O / Gene: VVM02027 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4V8GZL4*PLUS
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal growTemperature: 295 K / Method: microbatch / Details: sodium chloride, MES, PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→20.05 Å / Num. obs: 22720 / % possible obs: 99.9 % / Redundancy: 11.4 % / Biso Wilson estimate: 44.3 Å2 / Rrim(I) all: 0.073 / Net I/σ(I): 2.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3257 / Rrim(I) all: 1.073 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALAdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZXN

5zxn


Resolution: 2.2→20.05 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2374 1053 4.65 %
Rwork0.2009 21608 -
obs0.2027 22661 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.97 Å2 / Biso mean: 58.8025 Å2 / Biso min: 25.9 Å2
Refinement stepCycle: final / Resolution: 2.2→20.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 48 164 2709
Biso mean--41.4 57.66 -
Num. residues----337
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.30.39581260.332426462772
2.3-2.42110.38121230.300626372760
2.4211-2.57250.28261260.266326842810
2.5725-2.77060.29581150.241126742789
2.7706-3.04860.26711230.211626772800
3.0486-3.48770.22541440.189627012845
3.4877-4.38660.2041600.164727042864
4.3866-20.05050.20811360.177428853021
Refinement TLS params.Method: refined / Origin x: 13.234 Å / Origin y: -23.5241 Å / Origin z: -7.2753 Å
111213212223313233
T0.3694 Å2-0.0072 Å20.0613 Å2-0.4774 Å20.0185 Å2--0.3583 Å2
L3.2589 °20.1286 °2-0.968 °2-0.7287 °20.0123 °2--1.8122 °2
S-0.0329 Å °-0.8377 Å °-0.041 Å °0.2303 Å °0.0242 Å °0.0631 Å °-0.025 Å °0.2162 Å °0.0239 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 342
2X-RAY DIFFRACTION1allB2458
3X-RAY DIFFRACTION1allS2 - 185

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