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- PDB-6l5d: Crystal structure of the gas vesicle protein GvpF from Anabaena s... -

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Basic information

Entry
Database: PDB / ID: 6l5d
TitleCrystal structure of the gas vesicle protein GvpF from Anabaena sp. PCC7120
ComponentsGas vesicle protein
KeywordsSTRUCTURAL PROTEIN / gas vesicle / cyanobacteria
Function / homologygas vesicle / gas vesicle organization / Gas vesicle protein GvpL/GvpF / Gas vesicle synthesis protein GvpL/GvpF / Gas vesicle protein F
Function and homology information
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsCai, K. / Li, Q.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0400900 China
CitationJournal: Bmc Microbiol. / Year: 2020
Title: The model cyanobacteria Anabaena sp. PCC 7120 possess an intact but partially degenerated gene cluster encoding gas vesicles.
Authors: Cai, K. / Xu, B.Y. / Jiang, Y.L. / Wang, Y. / Chen, Y. / Zhou, C.Z. / Li, Q.
History
DepositionOct 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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
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: Gas vesicle protein
B: Gas vesicle protein


Theoretical massNumber of molelcules
Total (without water)58,5052
Polymers58,5052
Non-polymers00
Water50428
1
A: Gas vesicle protein


Theoretical massNumber of molelcules
Total (without water)29,2521
Polymers29,2521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Gas vesicle protein


Theoretical massNumber of molelcules
Total (without water)29,2521
Polymers29,2521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.400, 147.087, 106.579
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Gas vesicle protein


Mass: 29252.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: gvpF / Plasmid: pET-29a-derived / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YUT3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.33 Å3/Da / Density % sol: 63.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) polyethylene glycol 4000, 0.2 M NaCl, 0.1 M Tris-HCl, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 24900 / % possible obs: 99.9 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 16.3
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 2.875 / Num. unique obs: 2440 / Rsym value: 0.691 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QSG

4qsg


Resolution: 2.55→44.46 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.908 / SU B: 9.491 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.368 / ESU R Free: 0.274
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 1268 5.1 %RANDOM
Rwork0.1957 ---
obs0.1987 23603 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 153.67 Å2 / Biso mean: 53.189 Å2 / Biso min: 27.68 Å2
Baniso -1Baniso -2Baniso -3
1--3.89 Å2-0 Å20 Å2
2--1.66 Å2-0 Å2
3---2.23 Å2
Refinement stepCycle: final / Resolution: 2.55→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3962 0 0 28 3990
Biso mean---39.54 -
Num. residues----481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194052
X-RAY DIFFRACTIONr_bond_other_d0.0020.023866
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.9535476
X-RAY DIFFRACTIONr_angle_other_deg1.00538895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1745478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.64424.498209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.51315736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0661523
X-RAY DIFFRACTIONr_chiral_restr0.0950.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024547
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02966
LS refinement shellResolution: 2.554→2.62 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 86 -
Rwork0.276 1671 -
all-1757 -
obs--96.7 %

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