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- PDB-4we3: STRUCTURE OF THE BINARY COMPLEX OF A ZINGIBER OFFICINALE DOUBLE B... -

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Basic information

Entry
Database: PDB / ID: 4we3
TitleSTRUCTURE OF THE BINARY COMPLEX OF A ZINGIBER OFFICINALE DOUBLE BOND REDUCTASE IN COMPLEX WITH NADP MONOCLINIC CRYSTAL FORM
ComponentsDouble Bond Reductase
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD / TWISTED B-BARREL / CURCUMINOID REDUCTASE / PLANT PROTEIN
Function / homology
Function and homology information


2-alkenal reductase [NAD(P)+] activity / response to oxidative stress / nucleotide binding
Similarity search - Function
Medium-chain dehydrogenase/reductase / 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 ...Medium-chain dehydrogenase/reductase / 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 NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Zingiber officinale double bond reductase
Similarity search - Component
Biological speciesZingiber officinale (ginger)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsCollery, J. / Langlois d'Estaintot, B. / Buratto, J. / Granier, T. / Gallois, B. / Willis, M.A. / Sang, Y. / Flores-Sanchez, I.J. / Gang, D.R.
CitationJournal: to be published
Title: STRUCTURE OF ZINGIBER OFFICINALE DOUBLE BOND REDUCTASE
Authors: Buratto, J. / Langlois d'Estaintot, B. / Granier, T. / Gallois, B. / Willis, M.A. / Sang, Y. / Flores-Sanchez, I.J. / Gang, D.R.
History
DepositionSep 9, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name / _citation_author.name
Revision 1.2Jan 10, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Double Bond Reductase
B: Double Bond Reductase
C: Double Bond Reductase
D: Double Bond Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,9298
Polymers159,9564
Non-polymers2,9744
Water2,630146
1
A: Double Bond Reductase
B: Double Bond Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4654
Polymers79,9782
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-33 kcal/mol
Surface area26900 Å2
MethodPISA
2
C: Double Bond Reductase
D: Double Bond Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4654
Polymers79,9782
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-33 kcal/mol
Surface area27000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.704, 133.447, 90.942
Angle α, β, γ (deg.)90.000, 101.390, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA7 - 3487 - 348
21SERSERBB7 - 3487 - 348
12ARGARGAA7 - 3497 - 349
22ARGARGCC7 - 3497 - 349
13HISHISAA8 - 3578 - 357
23HISHISDD8 - 3588 - 357
14ARGARGBB7 - 3497 - 349
24ARGARGCC7 - 3497 - 349
15SERSERBB8 - 3488 - 348
25SERSERDD8 - 3488 - 348
16SERSERCC8 - 3488 - 348
26SERSERDD8 - 3488 - 348

NCS ensembles :
ID
1
2
3
4
5
6
DetailsThe biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D

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Components

#1: Protein
Double Bond Reductase


Mass: 39988.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zingiber officinale (ginger) / Plasmid: pEXP5-CT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A096LNF0*PLUS
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 1500 24%, PCB 100 mM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2014 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.49→46.4 Å / Num. all: 53557 / Num. obs: 53557 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.51 % / Biso Wilson estimate: 59.919 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.101 / Χ2: 1.019 / Net I/σ(I): 11.04 / Num. measured all: 243417
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.49-2.584.610.7470.9981.7424796541953721.12599.1
2.58-2.680.8350.7352.3924316524751930.82899
2.68-2.80.890.5493.124163524052170.6299.6
2.8-2.950.9410.3534.3624498550354760.499.5
2.95-3.140.9750.2216.624449552654950.25199.4
3.14-3.380.990.13910.1525028532853070.15799.6
3.38-3.720.9930.09713.7324264536053270.1199.4
3.72-4.260.9960.06618.2823378542053550.07598.8
4.26-5.360.9970.05323.2724526538853680.0699.6
5.360.9980.04126.3623999549154470.04799.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.49 Å46.4 Å
Translation2.49 Å46.4 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NH4

4nh4


Resolution: 2.6→46.4 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2575 / WRfactor Rwork: 0.2132 / FOM work R set: 0.7613 / SU R Cruickshank DPI: 1.1413 / SU Rfree: 0.3401 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.141 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2374 5 %RANDOM
Rwork0.2223 44714 --
obs0.2245 44714 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.07 Å2 / Biso mean: 49.76 Å2 / Biso min: 18.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å2-0 Å2-4.84 Å2
2---0.28 Å20 Å2
3---3.5 Å2
Refinement stepCycle: final / Resolution: 2.6→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10141 0 192 146 10479
Biso mean--46.12 42.13 -
Num. residues----1367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910593
X-RAY DIFFRACTIONr_bond_other_d00.029536
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.97914436
X-RAY DIFFRACTIONr_angle_other_deg3.775321839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86151356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55123.938419
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.616151501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0831533
X-RAY DIFFRACTIONr_chiral_restr0.0820.21605
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112101
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022452
X-RAY DIFFRACTIONr_mcbond_it3.535.1685457
X-RAY DIFFRACTIONr_mcbond_other3.5285.1675456
X-RAY DIFFRACTIONr_mcangle_it5.3657.746802
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A164280.1
12B164280.1
21A183160.11
22C183160.11
31A168480.11
32D168480.11
41B173650.1
42C173650.1
51B164370.1
52D164370.1
61C174680.1
62D174680.1
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 168 -
Rwork0.358 3278 -
all-3446 -
obs--99.39 %

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