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- PDB-2py2: Structure of Herring Type II Antifreeze Protein -

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Basic information

Entry
Database: PDB / ID: 2py2
TitleStructure of Herring Type II Antifreeze Protein
ComponentsAntifreeze protein type II
KeywordsANTIFREEZE PROTEIN / type II antifreeze protein
Function / homology
Function and homology information


signaling receptor activity / metal ion binding
Similarity search - Function
Type-2 ice-structuring protein / : / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) ...Type-2 ice-structuring protein / : / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesClupea harengus (Atlantic herring)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsLiu, Y. / Li, Z. / Lin, Q. / Seetharaman, J. / Sivaraman, J. / Hew, C.-L.
CitationJournal: PLoS ONE / Year: 2007
Title: Structure and Evolutionary Origin of Ca-Dependent Herring Type II Antifreeze Protein.
Authors: Liu, Y. / Li, Z. / Lin, Q. / Kosinski, J. / Seetharaman, J. / Bujnicki, J.M. / Sivaraman, J. / Hew, C.L.
History
DepositionMay 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Antifreeze protein type II
B: Antifreeze protein type II
C: Antifreeze protein type II
D: Antifreeze protein type II
E: Antifreeze protein type II
F: Antifreeze protein type II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,99112
Polymers92,7506
Non-polymers2406
Water10,467581
1
A: Antifreeze protein type II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4982
Polymers15,4581
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Antifreeze protein type II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4982
Polymers15,4581
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Antifreeze protein type II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4982
Polymers15,4581
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Antifreeze protein type II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4982
Polymers15,4581
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Antifreeze protein type II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4982
Polymers15,4581
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Antifreeze protein type II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4982
Polymers15,4581
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.279, 146.415, 192.406
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Antifreeze protein type II


Mass: 15458.392 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clupea harengus (Atlantic herring) / Gene: hAFP / Plasmid: pGAPZ alpha A / Production host: Pichia pastoris (fungus) / References: UniProt: Q91992
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 180 mM Ammonium Sulfate, 100 mM Sodium Acetate pH 4.5, 1mM Calcium Chloride, 20% PEG 4000 and 3% D-Glucose, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorDetector: CCD / Date: Sep 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 94813 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.9 % / Rsym value: 0.058

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 4543 -random
Rwork0.209 ---
all-99038 --
obs-90464 91.3 %-
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5976 0 6 581 6563

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