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- PDB-5yvf: Crystal structure of BFA1 -

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Basic information

Entry
Database: PDB / ID: 5yvf
TitleCrystal structure of BFA1
ComponentsBFA1
KeywordsPLANT PROTEIN / ATP synthase / assembly / fba1
Function / homologyDomain of unknown function DUF3598, Biogenesis factor required for ATP synthase 1-like / : / Domain of unknown function (DUF3598), N-terminal / Biogenesis factor required for ATP synthase 1, C-terminal domain / chloroplast fission / Calycin / Glutamate NMDA receptor subunit epsilon-1, putative (DUF3598) / Glutamate NMDA receptor subunit epsilon-1, putative (DUF3598)
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.804 Å
AuthorsPu, H. / Zhang, L. / Duan, Z.K. / Peng, L.W. / Liu, L.
CitationJournal: Plant Cell / Year: 2018
Title: Nucleus-Encoded Protein BFA1 Promotes Efficient Assembly of the Chloroplast ATP Synthase Coupling Factor 1.
Authors: Zhang, L. / Pu, H. / Duan, Z. / Li, Y. / Liu, B. / Zhang, Q. / Li, W. / Rochaix, J.D. / Liu, L. / Peng, L.
History
DepositionNov 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
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: BFA1
B: BFA1
C: BFA1
D: BFA1


Theoretical massNumber of molelcules
Total (without water)167,8084
Polymers167,8084
Non-polymers00
Water88349
1
A: BFA1


Theoretical massNumber of molelcules
Total (without water)41,9521
Polymers41,9521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BFA1


Theoretical massNumber of molelcules
Total (without water)41,9521
Polymers41,9521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BFA1


Theoretical massNumber of molelcules
Total (without water)41,9521
Polymers41,9521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: BFA1


Theoretical massNumber of molelcules
Total (without water)41,9521
Polymers41,9521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.925, 134.628, 149.477
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
BFA1


Mass: 41951.992 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g29185, AXX17_At3g32040
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A178VCD5, UniProt: F4J1U2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.17 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 0.1 M Bis-Tris, pH 6.3, 0.3 M MgCl2, 28% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 40170 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.049 / Rrim(I) all: 0.126 / Χ2: 1.122 / Net I/σ(I): 6.3 / Num. measured all: 293124
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.8-2.97.40.99139400.7240.3890.79999.6
2.9-3.027.40.66639490.8680.260.86899.70.715
3.02-3.157.40.44939460.9280.1760.95699.70.482
3.15-3.327.40.29639950.9620.1161.08299.70.319
3.32-3.537.40.20839630.9810.0821.16899.70.223
3.53-3.87.40.14839960.990.0581.14299.90.159
3.8-4.187.40.11140020.9940.0431.0899.90.119
4.18-4.797.30.07940390.9980.0311.09299.90.085
4.79-6.037.20.08840710.9960.0351.3561000.095
6.03-506.60.06842690.9980.0291.70899.60.074

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.804→46.728 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2609 2001 5 %
Rwork0.2209 --
obs0.2229 40030 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.2 Å2 / Biso mean: 30.8599 Å2 / Biso min: 10.91 Å2
Refinement stepCycle: final / Resolution: 2.804→46.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10074 0 0 49 10123
Biso mean---22.92 -
Num. residues----1270
LS refinement shellResolution: 2.804→2.8742 Å / Rfactor Rfree: 0.3647 / Rfactor Rwork: 0.3353
Refinement TLS params.Method: refined / Origin x: 29.5093 Å / Origin y: -0.996 Å / Origin z: -7.2642 Å
111213212223313233
T0.1331 Å2-0.0114 Å20.0007 Å2-0.148 Å2-0.0069 Å2--0.1331 Å2
L0.216 °20.0202 °20.1119 °2-0.2282 °20.0924 °2--0.1858 °2
S0.0581 Å °-0.015 Å °0.0547 Å °0.018 Å °-0.086 Å °0.0015 Å °0.042 Å °0.0059 Å °0.0178 Å °
Refinement TLS groupSelection details: all

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