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- PDB-5zxn: Crystal structure of CurA from Vibrio vulnificus -

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Basic information

Entry
Database: PDB / ID: 5zxn
TitleCrystal structure of CurA 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
NADP-dependent oxidoreductase
Similarity search - Component
Biological speciesVIBRIO VULNIFICUS MO6-24/O (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.855 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADP-dependent oxidoreductase
B: NADP-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0938
Polymers75,0552
Non-polymers1,0386
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-14 kcal/mol
Surface area27690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.516, 91.555, 104.792
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA4 - 343
211chain BB5 - 343

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Components

#1: Protein NADP-dependent oxidoreductase


Mass: 37527.496 Da / Num. of mol.: 2
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: A0A4V8GZL3*PLUS
#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.95 Å3/Da / Density % sol: 58.24 %
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: 0.9791 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: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.855→19.916 Å / Num. obs: 73918 / % possible obs: 99.4 % / Redundancy: 14.2 % / Biso Wilson estimate: 29.77 Å2 / Rrim(I) all: 0.117 / Net I/σ(I): 12.5
Reflection shellResolution: 1.855→1.96 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 10339 / Rrim(I) all: 1.621 / % possible all: 96.5

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.855→19.916 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.31
RfactorNum. reflection% reflection
Rfree0.2361 3726 5.05 %
Rwork0.2088 --
obs0.2102 73821 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.66 Å2 / Biso mean: 41.5972 Å2 / Biso min: 14.12 Å2
Refinement stepCycle: final / Resolution: 1.855→19.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5057 0 64 388 5509
Biso mean--45.8 41.13 -
Num. residues----679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085225
X-RAY DIFFRACTIONf_angle_d1.0857073
X-RAY DIFFRACTIONf_chiral_restr0.041765
X-RAY DIFFRACTIONf_plane_restr0.005923
X-RAY DIFFRACTIONf_dihedral_angle_d13.2881910
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2855X-RAY DIFFRACTION3.625TORSIONAL
12B2855X-RAY DIFFRACTION3.625TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.855-1.87850.34481240.32862345246990
1.8785-1.90320.31071720.29542445261796
1.9032-1.92920.31451220.2822526264898
1.9292-1.95670.34361440.266625652709100
1.9567-1.98590.29721350.269525992734100
1.9859-2.01690.25871340.255625772711100
2.0169-2.050.30681320.250125872719100
2.05-2.08530.34011160.249125992715100
2.0853-2.12320.2761270.235425832710100
2.1232-2.16390.25761330.227925952728100
2.1639-2.20810.25761450.213325852730100
2.2081-2.2560.26261410.221625822723100
2.256-2.30840.26321510.215225912742100
2.3084-2.36610.25161300.218225972727100
2.3661-2.42990.27791210.212326372758100
2.4299-2.50130.23941140.218225882702100
2.5013-2.58190.25291590.220325952754100
2.5819-2.67390.28051470.2226162763100
2.6739-2.78070.26721360.214725962732100
2.7807-2.90690.22771170.209926432760100
2.9069-3.05970.23141370.207526242761100
3.0597-3.25060.25481610.214825992760100
3.2506-3.50030.21031530.203826182771100
3.5003-3.85030.22031400.191126592799100
3.8503-4.40220.19831510.176526412792100
4.4022-5.52660.20121340.179926962830100
5.5266-19.91720.19391500.195328072957100

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