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- PDB-7jjv: Crystal waters on the nine polyproline type II helical bundle spr... -

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Basic information

Entry
Database: PDB / ID: 7jjv
TitleCrystal waters on the nine polyproline type II helical bundle springtail antifreeze protein from Granisotoma rainieri match the ice lattice
ComponentsGrAFP antifreeze protein
KeywordsANTIFREEZE PROTEIN / glycine-rich / polyproline type II
Biological speciesunclassified Entomobryomorpha (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsScholl, C.L. / Tsuda, S. / Graham, L.A. / Davies, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Febs J. / Year: 2021
Title: Crystal waters on the nine polyproline type II helical bundle springtail antifreeze protein from Granisotoma rainieri match the ice lattice.
Authors: Scholl, C.L. / Tsuda, S. / Graham, L.A. / Davies, P.L.
History
DepositionJul 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: 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 1.2Oct 18, 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GrAFP antifreeze protein
B: GrAFP antifreeze protein


Theoretical massNumber of molelcules
Total (without water)21,6222
Polymers21,6222
Non-polymers00
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-19 kcal/mol
Surface area9710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.489, 64.214, 86.267
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 GrAFP antifreeze protein


Mass: 10811.161 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unclassified Entomobryomorpha (arthropod)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.95 Å3/Da / Density % sol: 37.01 %
Crystal growTemperature: 277.15 K / Method: microbatch / Details: 0.2 M lithium nitrate, 2.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.21→43.171 Å / Num. obs: 52608 / % possible obs: 99.9 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.019 / Rrim(I) all: 0.067 / Χ2: 0.9 / Net I/σ(I): 16.5
Reflection shellResolution: 1.21→1.23 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.925 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2579 / CC1/2: 0.923 / Rpim(I) all: 0.266 / Rrim(I) all: 0.963 / Χ2: 0.76 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIXv1.18refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PNE

2pne


Resolution: 1.21→43.171 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.452 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.04
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1804 2636 5.016 %
Rwork0.1489 49918 -
all0.151 --
obs-52554 99.846 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.855 Å2
Baniso -1Baniso -2Baniso -3
1-1.659 Å20 Å2-0 Å2
2---1.163 Å20 Å2
3----0.496 Å2
Refinement stepCycle: LAST / Resolution: 1.21→43.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 0 229 1610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0131445
X-RAY DIFFRACTIONr_bond_other_d0.0110.0181215
X-RAY DIFFRACTIONr_angle_refined_deg2.1151.6231951
X-RAY DIFFRACTIONr_angle_other_deg2.0851.6012858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9075263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.8443029
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51815130
X-RAY DIFFRACTIONr_chiral_restr0.0880.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021970
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02250
X-RAY DIFFRACTIONr_nbd_refined0.1660.2362
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.21220
X-RAY DIFFRACTIONr_nbtor_refined0.1520.2850
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.2840
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2114
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.170.225
X-RAY DIFFRACTIONr_nbd_other0.2010.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1920.213
X-RAY DIFFRACTIONr_mcbond_it2.4081.6571037
X-RAY DIFFRACTIONr_mcbond_other2.3961.6531036
X-RAY DIFFRACTIONr_mcangle_it2.9632.4821305
X-RAY DIFFRACTIONr_mcangle_other2.9622.4871306
X-RAY DIFFRACTIONr_scbond_it4.2232.438408
X-RAY DIFFRACTIONr_scbond_other4.2072.417406
X-RAY DIFFRACTIONr_scangle_it4.3043.418646
X-RAY DIFFRACTIONr_scangle_other4.3043.417646
X-RAY DIFFRACTIONr_lrange_it4.02324.5821702
X-RAY DIFFRACTIONr_lrange_other3.91223.7461649
X-RAY DIFFRACTIONr_rigid_bond_restr5.74632660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.2410.2612050.2563632X-RAY DIFFRACTION99.6623
1.241-1.2750.2261950.2243525X-RAY DIFFRACTION99.7052
1.275-1.3120.2321900.2013447X-RAY DIFFRACTION99.7532
1.312-1.3530.1861810.1833315X-RAY DIFFRACTION99.9714
1.353-1.3970.1661670.1613311X-RAY DIFFRACTION99.9138
1.397-1.4460.1731670.1423136X-RAY DIFFRACTION99.7584
1.446-1.5010.1751520.1333031X-RAY DIFFRACTION99.9372
1.501-1.5620.1511550.1212937X-RAY DIFFRACTION99.9031
1.562-1.6310.1451340.1132832X-RAY DIFFRACTION100
1.631-1.7110.1491530.1132697X-RAY DIFFRACTION99.9299
1.711-1.8030.1381370.1062580X-RAY DIFFRACTION99.853
1.803-1.9120.15950.1162481X-RAY DIFFRACTION99.9612
1.912-2.0440.1611360.1232289X-RAY DIFFRACTION100
2.044-2.2080.129980.122163X-RAY DIFFRACTION99.8234
2.208-2.4180.171030.1261990X-RAY DIFFRACTION100
2.418-2.7030.1571020.1431810X-RAY DIFFRACTION99.8433
2.703-3.1190.175940.1491593X-RAY DIFFRACTION99.7045
3.119-3.8170.228770.1451392X-RAY DIFFRACTION99.7962
3.817-5.3830.185620.1711084X-RAY DIFFRACTION99.6522
5.383-43.1710.369320.306656X-RAY DIFFRACTION99.2785

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