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- PDB-5zt3: Crystal structure of WA352 from Oryza sativa -

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Basic information

Entry
Database: PDB / ID: 5zt3
TitleCrystal structure of WA352 from Oryza sativa
ComponentsWA352
KeywordsPLANT PROTEIN / Cytoplasmic male sterility protein
Function / homology: / mitochondrion / membrane / Uncharacterized protein orf297 / Transmembrane protein
Function and homology information
Biological speciesOryza sativa subsp. indica (long-grained rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.304 Å
AuthorsWang, X. / Guan, Z. / Yin, P.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Crystal structure of WA352 provides insight into cytoplasmic male sterility in rice
Authors: Wang, X. / Guan, Z. / Gong, Z. / Yan, J. / Yang, G. / Liu, Y.G. / Yin, P.
History
DepositionMay 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: WA352


Theoretical massNumber of molelcules
Total (without water)14,8881
Polymers14,8881
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6910 Å2
Unit cell
Length a, b, c (Å)33.849, 35.435, 95.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein WA352


Mass: 14887.684 Da / Num. of mol.: 1 / Fragment: UNP residues 163-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. indica (long-grained rice)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H5ZXG7, UniProt: M1SWB3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 1.92 Å3/Da / Density % sol: 36.07 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: PEG 3000, Calcium acetate, Tris base/ Hydrochloric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 192774 / % possible obs: 98.4 % / Redundancy: 6.8 % / Net I/σ(I): 12.1
Reflection shellResolution: 1.3→1.33 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.304→28.458 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.88
RfactorNum. reflection% reflection
Rfree0.1932 1378 4.87 %
Rwork0.1877 --
obs0.1881 28310 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.304→28.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 0 0 132 1054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005941
X-RAY DIFFRACTIONf_angle_d0.7351272
X-RAY DIFFRACTIONf_dihedral_angle_d19.554358
X-RAY DIFFRACTIONf_chiral_restr0.065133
X-RAY DIFFRACTIONf_plane_restr0.005169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3036-1.35020.27021270.25062603X-RAY DIFFRACTION97
1.3502-1.40430.2311480.22472694X-RAY DIFFRACTION100
1.4043-1.46820.21411660.19882679X-RAY DIFFRACTION100
1.4682-1.54560.21491240.182724X-RAY DIFFRACTION100
1.5456-1.64240.20271300.17952690X-RAY DIFFRACTION100
1.6424-1.76920.19031330.18092743X-RAY DIFFRACTION100
1.7692-1.94720.19161240.17992727X-RAY DIFFRACTION100
1.9472-2.22890.17161320.16722771X-RAY DIFFRACTION100
2.2289-2.80770.17651580.18132763X-RAY DIFFRACTION100
2.8077-28.46490.19981360.19712538X-RAY DIFFRACTION87
Refinement TLS params.Method: refined / Origin x: 38.4672 Å / Origin y: 39.1867 Å / Origin z: 110.3341 Å
111213212223313233
T0.1074 Å20.0039 Å20.014 Å2-0.1141 Å2-0.0045 Å2--0.1237 Å2
L0.1654 °20.0103 °20.1711 °2-0.5873 °2-0.6051 °2--1.2103 °2
S0.0284 Å °0.0027 Å °-0.0467 Å °0.0052 Å °-0.0382 Å °0.034 Å °0.0484 Å °0.082 Å °-0.0008 Å °
Refinement TLS groupSelection details: all

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