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- PDB-3bog: Snow Flea Antifreeze Protein Quasi-racemate -

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Basic information

Entry
Database: PDB / ID: 3bog
TitleSnow Flea Antifreeze Protein Quasi-racemate
Components(6.5 kDa glycine-rich antifreeze protein) x 2
KeywordsANTIFREEZE PROTEIN / quasi-racemate / sfAFP / mirror image proteins / racemic protein crystallography
Function / homologyUnknown ligand / 6.5 kDa glycine-rich antifreeze protein
Function and homology information
Biological speciesHypogastrura harveyi (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 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
DepositionDec 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jan 24, 2018Group: Polymer sequence / Source and taxonomy / Structure summary
Category: audit_author / entity_poly / pdbx_entity_src_syn
Item: _audit_author.name / _entity_poly.pdbx_seq_one_letter_code_can ..._audit_author.name / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 2.1Aug 21, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly_prop.value / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
B: 6.5 kDa glycine-rich antifreeze protein
C: 6.5 kDa glycine-rich antifreeze protein
D: 6.5 kDa glycine-rich antifreeze protein


Theoretical massNumber of molelcules
Total (without water)26,1395
Polymers26,1394
Non-polymers01
Water8,215456
1
A: 6.5 kDa glycine-rich antifreeze protein

D: 6.5 kDa glycine-rich antifreeze protein


Theoretical massNumber of molelcules
Total (without water)13,0702
Polymers13,0702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area840 Å2
ΔGint-8 kcal/mol
Surface area6900 Å2
MethodPISA
2
B: 6.5 kDa glycine-rich antifreeze protein

C: 6.5 kDa glycine-rich antifreeze protein


Theoretical massNumber of molelcules
Total (without water)13,0703
Polymers13,0702
Non-polymers01
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area840 Å2
ΔGint-8 kcal/mol
Surface area7250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.640, 32.359, 59.699
Angle α, β, γ (deg.)88.62, 89.31, 72.84
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 6.5 kDa glycine-rich antifreeze protein


Mass: 6582.798 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The protein was chemically synthesized. / Source: (synth.) Hypogastrura harveyi (arthropod) / References: UniProt: Q38PT6
#2: Protein 6.5 kDa glycine-rich antifreeze protein


Mass: 6486.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The protein was chemically synthesized. / Source: (synth.) Hypogastrura harveyi (arthropod) / References: UniProt: Q38PT6
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.03 Å3/Da / Density % sol: 39.43 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97928, 0.97942, 0.94929
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 30, 2007
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979281
20.979421
30.949291
ReflectionResolution: 1.2→50 Å / Num. obs: 57496 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 37.9
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 9.9 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXD(heavy atom search)phasing
SOLVE(MAD phasing and density modification)phasing
RESOLVE(MAD phasing and density modification)phasing
RefinementMethod to determine structure: MAD / Resolution: 1.2→27.36 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.942 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.192 3064 5.1 %RANDOM
Rwork0.16 ---
obs0.162 57496 94.7 %-
all-57496 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20.02 Å20.25 Å2
2--0.29 Å2-0.1 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.2→27.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1818 0 8 477 2303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191861
X-RAY DIFFRACTIONr_bond_other_d0.0030.021367
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.9452492
X-RAY DIFFRACTIONr_angle_other_deg1.0052.2133179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.2845320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.19825.55618
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6351588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.838152
X-RAY DIFFRACTIONr_chiral_restr0.0770.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022472
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02352
X-RAY DIFFRACTIONr_nbd_refined0.1980.2584
X-RAY DIFFRACTIONr_nbd_other0.1930.21496
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21163
X-RAY DIFFRACTIONr_nbtor_other0.0970.21052
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.2124
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.253
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9171.51513
X-RAY DIFFRACTIONr_mcbond_other0.9731.5762
X-RAY DIFFRACTIONr_mcangle_it2.51922231
X-RAY DIFFRACTIONr_scbond_it3.6023357
X-RAY DIFFRACTIONr_scangle_it4.5764.5261
X-RAY DIFFRACTIONr_rigid_bond_restr1.75331667
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded4.59731640
LS refinement shellResolution: 1.2→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 208 -
Rwork0.137 4052 -
obs--90.54 %

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