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- PDB-7q3v: Re-refined structure of a type III antifreeze protein isoform HPLC 12 -

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Basic information

Entry
Database: PDB / ID: 7q3v
TitleRe-refined structure of a type III antifreeze protein isoform HPLC 12
ComponentsType-3 ice-structuring protein HPLC 12
KeywordsANTIFREEZE PROTEIN / restrained MD refinement scheme / Amber / crystal unit cell model / ensemble refinement
Function / homologyAntifreeze, type III / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain superfamily / extracellular region / Type-3 ice-structuring protein HPLC 12
Function and homology information
Biological speciesZoarces americanus (ocean pout)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMikhailovskii, O. / Xue, Y. / Jia, Z. / Skrynnikov, N.R.
Funding support Russian Federation, China, 3items
OrganizationGrant numberCountry
Russian Science Foundation21-44-00033 Russian Federation
St. Petersburg State University72777155 Russian Federation
National Science Foundation (NSF, China)32061133011 China
CitationJournal: Iucrj / Year: 2022
Title: Modeling a unit cell: crystallographic refinement procedure using the biomolecular MD simulation platform Amber.
Authors: Mikhailovskii, O. / Xue, Y. / Skrynnikov, N.R.
History
DepositionOct 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type-3 ice-structuring protein HPLC 12
B: Type-3 ice-structuring protein HPLC 12
C: Type-3 ice-structuring protein HPLC 12
D: Type-3 ice-structuring protein HPLC 12


Theoretical massNumber of molelcules
Total (without water)28,2264
Polymers28,2264
Non-polymers00
Water2,792155
1
A: Type-3 ice-structuring protein HPLC 12


Theoretical massNumber of molelcules
Total (without water)7,0561
Polymers7,0561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type-3 ice-structuring protein HPLC 12


Theoretical massNumber of molelcules
Total (without water)7,0561
Polymers7,0561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Type-3 ice-structuring protein HPLC 12


Theoretical massNumber of molelcules
Total (without water)7,0561
Polymers7,0561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Type-3 ice-structuring protein HPLC 12


Theoretical massNumber of molelcules
Total (without water)7,0561
Polymers7,0561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.270, 39.890, 44.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Type-3 ice-structuring protein HPLC 12 / Antifreeze protein QAE(HPLC 12) / ISP type III HPLC 12


Mass: 7056.444 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zoarces americanus (ocean pout) / Production host: Escherichia coli (E. coli) / Strain (production host): JM 83 / References: UniProt: P19614
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.09 Å3/Da / Density % sol: 30 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50-55% AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4-4.5

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 11, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→14.86 Å / Num. obs: 19230 / % possible obs: 99.1 % / Redundancy: 3.8 % / Rsym value: 0.077 / Net I/σ(I): 7.8
Reflection shellResolution: 1.9→1.97 Å / Rsym value: 0.306 / % possible all: 98.3

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Processing

Software
NameClassification
AMBERrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MSI

1msi


Resolution: 1.9→14.86 Å / Cross valid method: FREE R-VALUE / Phase error: 21.18
Details: The original structure, 2MSI, has been expanded into a crystal unit cell (containing four protein chains); the resulting model was subsequently refined through a specially designed ...Details: The original structure, 2MSI, has been expanded into a crystal unit cell (containing four protein chains); the resulting model was subsequently refined through a specially designed constrained MD run using a customized version of the program Amber. Note: ordered water molecules are added after the refinement using the standard water-picking facility of phenix.refine.
RfactorNum. reflection% reflectionSelection details
Rfree0.1943 1749 9.87 %random
Rwork0.1597 ---
obs0.1632 17720 99.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.39 Å2 / Biso mean: 20.1134 Å2 / Biso min: 6.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→14.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 0 155 2107
LS refinement shellResolution: 1.9→1.96 Å
RfactorNum. reflection% reflection
Rfree0.2499 134 -
Rwork0.1904 1284 -
obs--98 %

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