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- PDB-9cbe: Structure of a type III antifreeze protein isoform HPLC12 re-refi... -

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Basic information

Entry
Database: PDB / ID: 9cbe
TitleStructure of a type III antifreeze protein isoform HPLC12 re-refined using standard protocols
ComponentsType-3 ice-structuring protein HPLC 12
KeywordsANTIFREEZE PROTEIN / Re-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 / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsWlodawer, A. / Dauter, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J.Mol.Biol. / Year: 1998
Title: The effects of steric mutations on the structure of type III antifreeze protein and its interaction with ice.
Authors: DeLuca, C.I. / Davies, P.L. / Ye, Q. / Jia, Z.
History
DepositionJun 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Remark 0THIS ENTRY 9CBE REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 2MSI, DETERMINED BY C.I. ...THIS ENTRY 9CBE REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 2MSI, DETERMINED BY C.I.DELUCA,P.L.DAVIES,Q.YE,Z.JIA

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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


Theoretical massNumber of molelcules
Total (without water)7,0991
Polymers7,0991
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.270, 39.890, 44.540
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 Type-3 ice-structuring protein HPLC 12 / Antifreeze protein QAE(HPLC 12) / ISP type III HPLC 12


Mass: 7099.468 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zoarces americanus (ocean pout) / Production host: Escherichia coli (E. coli) / References: UniProt: P19614
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growDetails: PROTEIN WAS CRYSTALLIZED IN 50-55% AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4-4.5
PH range: 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→8 Å / Num. obs: 4933 / % possible obs: 99.1 % / Observed criterion σ(I): 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
NameVersionClassification
REFMAC5.8.0258refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→8 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.751 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18908 262 5.3 %RANDOM
Rwork0.15001 ---
obs0.15215 4637 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms491 0 0 39 530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.013501
X-RAY DIFFRACTIONr_bond_other_d0.0010.017511
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.65685
X-RAY DIFFRACTIONr_angle_other_deg1.3341.5581185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.307565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07722.77818
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2061591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.014153
X-RAY DIFFRACTIONr_chiral_restr0.0830.273
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02539
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0278
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8681.756263
X-RAY DIFFRACTIONr_mcbond_other1.831.737262
X-RAY DIFFRACTIONr_mcangle_it2.9762.599327
X-RAY DIFFRACTIONr_mcangle_other32.618328
X-RAY DIFFRACTIONr_scbond_it3.5492.255238
X-RAY DIFFRACTIONr_scbond_other3.5292.25238
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5853.179358
X-RAY DIFFRACTIONr_long_range_B_refined7.29821.763502
X-RAY DIFFRACTIONr_long_range_B_other7.34221.756500
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.905→1.953 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 14 -
Rwork0.169 319 -
obs--98.52 %

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