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- PDB-6l2w: Crystal structure of a novel fold protein Gp72 from the freshwate... -

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Basic information

Entry
Database: PDB / ID: 6l2w
TitleCrystal structure of a novel fold protein Gp72 from the freshwater cyanophage Mic1
Componentsfreshwater cyanophage protein
KeywordsSTRUCTURAL PROTEIN / hypothetical proteins
Function / homologyUncharacterized protein
Function and homology information
Biological speciesMicrocystis phage Mic1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.29 Å
AuthorsWang, Y. / Jin, H. / Yang, F. / Jiang, Y.L. / Zhao, Y.Y. / Chen, Z.P. / Li, W.F. / Chen, Y. / Zhou, C.Z. / Li, Q.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China31630001 China
National Natural Science Foundation of China31621002 China
Ministry of Science and Technology (China)2018YFA0903100 China
Ministry of Science and Technology (China)2016YFA0400900 China
Chinese Academy of Sciences China
CitationJournal: Proteins / Year: 2020
Title: Crystal structure of a novel fold protein Gp72 from the freshwater cyanophage Mic1.
Authors: Wang, Y. / Jin, H. / Yang, F. / Jiang, Y.L. / Zhao, Y.Y. / Chen, Z.P. / Li, W.F. / Chen, Y. / Zhou, C.Z. / Li, Q.
History
DepositionOct 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: 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: freshwater cyanophage protein
B: freshwater cyanophage protein


Theoretical massNumber of molelcules
Total (without water)29,2732
Polymers29,2732
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-13 kcal/mol
Surface area13010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.702, 45.534, 67.368
Angle α, β, γ (deg.)90.000, 94.290, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-201-

HOH

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Components

#1: Protein freshwater cyanophage protein


Mass: 14636.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microcystis phage Mic1 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A4Y5TR47
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 13% polyethylene glycol 6000, 0.1 M ADA pH 7.0, 0.01 M spermine tetrahydrochloride and 0.1 M guanidine hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 11607 / % possible obs: 98.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 25.23
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 1125

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.29→42.77 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.901 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.368 / ESU R Free: 0.236
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 526 4.5 %RANDOM
Rwork0.1994 ---
obs0.2012 11081 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 114.34 Å2 / Biso mean: 53.241 Å2 / Biso min: 29.47 Å2
Baniso -1Baniso -2Baniso -3
1--2.45 Å2-0 Å20.8 Å2
2--5.44 Å20 Å2
3----3.08 Å2
Refinement stepCycle: final / Resolution: 2.29→42.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1919 0 0 57 1976
Biso mean---50.03 -
Num. residues----234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0151956
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171724
X-RAY DIFFRACTIONr_angle_refined_deg1.2391.72636
X-RAY DIFFRACTIONr_angle_other_deg0.461.7134038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9945231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.04821.07765
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.3215278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.031156
X-RAY DIFFRACTIONr_chiral_restr0.0570.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022180
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02380
LS refinement shellResolution: 2.29→2.347 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.396 35 -
Rwork0.33 654 -
obs--80.68 %

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