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- PDB-2pne: Crystal Structure of the Snow Flea Antifreeze Protein -

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Basic information

Entry
Database: PDB / ID: 2pne
TitleCrystal Structure of the Snow Flea Antifreeze Protein
Components6.5 kDa glycine-rich antifreeze protein
KeywordsANTIFREEZE PROTEIN / chemical protein synthesis / native chemical ligation
Function / homology6.5 kDa glycine-rich antifreeze protein
Function and homology information
Biological speciesHypogastrura harveyi (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsPentelute, B.L. / Kent, S.B.H. / Gates, Z.P. / Tereshko, V. / Kossiakoff, A.A. / Kurutz, J. / Dashnau, J. / Vaderkooi, J.M.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: X-ray structure of snow flea antifreeze protein determined by racemic crystallization of synthetic protein enantiomers
Authors: Pentelute, B.L. / Gates, Z.P. / Tereshko, V. / Dashnau, J.L. / Vanderkooi, J.M. / Kossiakoff, A.A. / Kent, S.B.
History
DepositionApr 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Structure summary / Category: audit_author / pdbx_entity_src_syn
Item: _audit_author.name / _pdbx_entity_src_syn.details ..._audit_author.name / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Aug 30, 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 1.4Oct 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: 6.5 kDa glycine-rich antifreeze protein


Theoretical massNumber of molelcules
Total (without water)6,4901
Polymers6,4901
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)16.699, 74.281, 17.687
Angle α, β, γ (deg.)90.00, 102.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 6.5 kDa glycine-rich antifreeze protein


Mass: 6489.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Prepared by total chemical synthesis. / Source: (synth.) Hypogastrura harveyi (arthropod) / References: UniProt: Q38PT6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 1.65 Å3/Da / Density % sol: 25.7 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918
DetectorDetector: CCD / Date: Dec 3, 2006
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 0.95→50 Å / Num. obs: 23972 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 17.9
Reflection shellResolution: 0.95→0.98 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3 / % possible all: 46

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BOG

3bog


Resolution: 0.98→17.29 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.818 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.164 1173 5.1 %RANDOM
Rwork0.14 ---
obs0.141 21783 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.79 Å2
2---0.79 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 0.98→17.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms453 0 0 113 566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021462
X-RAY DIFFRACTIONr_bond_other_d0.0010.02306
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.966619
X-RAY DIFFRACTIONr_angle_other_deg0.8653.011741
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.229580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.412610
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.9831540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.307151
X-RAY DIFFRACTIONr_chiral_restr0.1120.251
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02615
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0282
X-RAY DIFFRACTIONr_nbd_refined0.1980.2107
X-RAY DIFFRACTIONr_nbd_other0.1830.2339
X-RAY DIFFRACTIONr_nbtor_refined0.160.2267
X-RAY DIFFRACTIONr_nbtor_other0.0830.2237
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.270
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2120.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4291.5380
X-RAY DIFFRACTIONr_mcbond_other1.1471.5193
X-RAY DIFFRACTIONr_mcangle_it1.9382552
X-RAY DIFFRACTIONr_scbond_it2.685388
X-RAY DIFFRACTIONr_scangle_it3.5414.567
X-RAY DIFFRACTIONr_rigid_bond_restr1.343468
X-RAY DIFFRACTIONr_sphericity_free9.026386
X-RAY DIFFRACTIONr_sphericity_bonded4.6163453
LS refinement shellResolution: 0.98→1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 69 -
Rwork0.303 1368 -
obs--83.55 %

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