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- PDB-4nh4: Structure of the binary complex of a zingiber officinale double b... -

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Basic information

Entry
Database: PDB / ID: 4nh4
TitleStructure of the binary complex of a zingiber officinale double bond reductase in complex with NADP
ComponentsZingiber officinale double bond reductase
KeywordsPLANT PROTEIN / ROSSMANN FOLD / TWISTED B-BARREL / CURCUMINOID REDUCTASE
Function / homology
Function and homology information


2-alkenal reductase [NAD(P)H] activity / nucleotide binding
Similarity search - Function
Oxidoreductase, N-terminal domain / Medium-chain dehydrogenase/reductase / 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 ...Oxidoreductase, N-terminal domain / Medium-chain dehydrogenase/reductase / 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: 2.1 Å
AuthorsLanglois 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
DepositionNov 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zingiber officinale double bond reductase
B: Zingiber officinale double bond reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4654
Polymers79,9782
Non-polymers1,4872
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-20 kcal/mol
Surface area28990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.660, 78.406, 155.706
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Zingiber officinale double bond reductase


Mass: 39988.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ZINGIBER OFFICINALE (ginger) / Plasmid: PEXP5-CT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CODONPLUS-RP / References: UniProt: A0A096LNF0*PLUS
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.31 Å3/Da / Density % sol: 46.86 % / Mosaicity: 0.18 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 21% PEG 1450, 100mM PCB, 3mM NaN3, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 3, 2013 / Details: PT COATED SI MIRRORS
RadiationMonochromator: HORIZONTALLY SIDE DIFFRACTING SILICON 111 CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.1→78.037 Å / Num. all: 43868 / Num. obs: 43868 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rsym value: 0.091 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.1-2.214.60.8430.7450.92891663100.3890.8430.7452.499.9
2.21-2.354.40.6970.6112589059250.330.6970.613.298
2.35-2.514.60.3840.3392.32600356620.1770.3840.3394.599.9
2.51-2.714.50.2740.2413.22335552430.1290.2740.2416.298.9
2.71-2.974.60.1680.1485.22238448720.0770.1680.1489.2100
2.97-3.324.60.0920.0829.42035344580.0430.0920.08215.7100
3.32-3.834.30.060.05313.71657138840.0290.060.05323.798.4
3.83-4.74.30.040.03519.51427333210.0190.040.03533.598.3
4.7-6.644.40.0350.03121.71165026540.0160.0350.03133.5100
6.64-55.2454.10.0250.02226.9630215390.0120.0250.02239.999.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.21data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MKR

4mkr


Resolution: 2.1→55.31 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.2285 / WRfactor Rwork: 0.1671 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7934 / SU B: 12.393 / SU ML: 0.169 / SU R Cruickshank DPI: 0.2343 / SU Rfree: 0.2088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.209 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2598 2250 5.1 %RANDOM
Rwork0.193 ---
all0.1964 43787 --
obs0.1964 43787 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.83 Å2 / Biso mean: 39.061 Å2 / Biso min: 14.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.45 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.1→55.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5391 0 96 337 5824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195640
X-RAY DIFFRACTIONr_bond_other_d0.0010.025259
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.9817668
X-RAY DIFFRACTIONr_angle_other_deg0.848312090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0325702
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73724.128235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68815888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6971519
X-RAY DIFFRACTIONr_chiral_restr0.0990.2843
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021294
X-RAY DIFFRACTIONr_mcbond_it2.132.4752811
X-RAY DIFFRACTIONr_mcbond_other2.132.4742810
X-RAY DIFFRACTIONr_mcangle_it3.1524.1533509
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 165 -
Rwork0.29 3031 -
all-3196 -
obs--99.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.88680.6924-0.82840.9525-1.00721.1570.26420.18730.23050.20990.01180.1981-0.1834-0.1373-0.2760.33540.00190.11040.210.08630.1352-12.74436.00864.947
22.03860.1167-0.85680.4673-0.16380.99460.2044-0.09050.01660.1846-0.12250.0217-0.16460.1506-0.08190.3576-0.09520.01610.10650.01610.029913.12836.36663.242
31.51920.18810.98051.11510.27711.7294-0.01830.2069-0.00610.23550.082-0.1159-0.08530.1684-0.06370.25880.0175-0.03170.1708-0.02460.08942.12938.66924.009
41.1767-0.189-0.9740.3126-0.25291.63370.14410.46590.09450.1212-0.0865-0.0646-0.1697-0.4125-0.05750.25190.0918-0.01320.36830.08510.05212.3939.78831.608
51.91920.11120.31181.604-0.3942.091-0.23040.3230.01780.0930.18110.0259-0.1737-0.19160.04940.25840.0564-0.00270.13770.00440.055728.16337.01318.168
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 127
2X-RAY DIFFRACTION2A128 - 352
3X-RAY DIFFRACTION3B7 - 139
4X-RAY DIFFRACTION4B140 - 294
5X-RAY DIFFRACTION5B295 - 351

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