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- PDB-7eoz: The structure of rice Defective Pollen Wall (DPW) in the complex ... -

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Basic information

Entry
Database: PDB / ID: 7eoz
TitleThe structure of rice Defective Pollen Wall (DPW) in the complex with its cofactor NADP
ComponentsFatty acyl-CoA reductase
KeywordsOXIDOREDUCTASE / fatty acyl carrier protein reductase / UDP-glucose epimerase / lipid and sugar metabolisms / NADP+ / plant / LIPID BINDING PROTEIN
Function / homology
Function and homology information


alcohol-forming fatty acyl-CoA reductase / alcohol-forming very long-chain fatty acyl-CoA reductase activity / alcohol-forming long-chain fatty acyl-CoA reductase activity / lipid metabolic process
Similarity search - Function
Fatty acyl-CoA reductase / Fatty acyl-CoA reductase, C-terminal / Male sterility protein / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Fatty acyl-CoA reductase
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å
AuthorsYan, L.M. / Wang, W. / Li, G. / Wang, J.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2017YFC0840300 China
CitationJournal: To Be Published
Title: Defective Pollen Wall Bridges Lipid and Sugar Metabolisms in Plant Male Reproductive Development
Authors: Wang, W. / Li, G. / Wang, J. / Yan, L.M.
History
DepositionApr 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acyl-CoA reductase
B: Fatty acyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,4144
Polymers115,9272
Non-polymers1,4872
Water1,53185
1
A: Fatty acyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7072
Polymers57,9641
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty acyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7072
Polymers57,9641
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)222.814, 222.814, 114.024
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Fatty acyl-CoA reductase


Mass: 57963.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: OSJNBa0091P11.14, Os03g0167600 / Production host: Escherichia coli (E. coli)
References: UniProt: Q0DUU1, alcohol-forming fatty acyl-CoA reductase
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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

Crystal growTemperature: 291 K / Method: evaporation
Details: 2.8 M sodium formate, pH 7.0, 0.1 M magnesium chloride hexahydrate, 0.1 M HEPES, pH 7.5, 5% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 48784 / % possible obs: 99.8 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.136 / Χ2: 5.755 / Net I/σ(I): 16 / Num. measured all: 540754
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3.3-3.3610.90.78824112.7981100
3.36-3.42110.64724173.021100
3.42-3.48110.5624512.9231100
3.48-3.5511.10.44124303.3461100
3.55-3.6311.10.42324343.4871100
3.63-3.7211.30.29724353.7271100
3.72-3.8111.20.31424254.0021100
3.81-3.9111.30.23724413.9651100
3.91-4.0311.20.22223954.5431100
4.03-4.1611.20.18724615.5051100
4.16-4.3111.30.16624316.21100
4.31-4.4811.20.14124566.5881100
4.48-4.6811.20.12824167.4151100
4.68-4.9311.20.1224557.5311100
4.93-5.2411.30.11624618.1261100
5.24-5.6411.30.10924317.2841100
5.64-6.2111.30.09324786.6361100
6.21-7.111.30.08224537.1351100
7.1-8.94110.06424818.108199.9
8.94-509.40.057242213.847195.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.4→48.45 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.907 / SU B: 15.94 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.559 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2396 2223 5.1 %RANDOM
Rwork0.1913 ---
obs0.1938 41278 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 264.51 Å2 / Biso mean: 94.95 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å20 Å2
2--0.05 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 3.4→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7435 0 96 85 7616
Biso mean--85.98 88.72 -
Num. residues----955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137692
X-RAY DIFFRACTIONr_bond_other_d0.0020.0157248
X-RAY DIFFRACTIONr_angle_refined_deg2.181.64210417
X-RAY DIFFRACTIONr_angle_other_deg1.3291.57916639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.0955949
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31821.418409
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.142151265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3631558
X-RAY DIFFRACTIONr_chiral_restr0.0890.2992
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028721
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021813
LS refinement shellResolution: 3.4→3.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 166 -
Rwork0.349 3018 -
all-3184 -
obs--96.98 %

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