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- PDB-1l0s: Choristoneura fumiferana (spruce budworm) antifreeze protein isof... -

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Basic information

Entry
Database: PDB / ID: 1l0s
TitleChoristoneura fumiferana (spruce budworm) antifreeze protein isoform 337
Componentsthermal hysteresis protein
KeywordsANTIFREEZE PROTEIN / left-handed beta-helix / iodination
Function / homologyChoristoneura fumiferana antifreeze / Insect antifreeze protein superfamily / Choristoneura fumiferana antifreeze protein (CfAFP) / Insect antifreeze protein / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Mainly Beta / : / Thermal hysteresis protein
Function and homology information
Biological speciesChoristoneura fumiferana (eastern spruce budworm)
MethodX-RAY DIFFRACTION / SAS / Resolution: 2.3 Å
AuthorsLeinala, E.K. / Davies, P.L. / Jia, Z.
CitationJournal: Structure / Year: 2002
Title: Crystal structure of beta-helical antifreeze protein points to a general ice binding model.
Authors: Leinala, E.K. / Davies, P.L. / Jia, Z.
History
DepositionFeb 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: thermal hysteresis protein
B: thermal hysteresis protein
C: thermal hysteresis protein
D: thermal hysteresis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4406
Polymers37,2154
Non-polymers2252
Water3,261181
1
A: thermal hysteresis protein


Theoretical massNumber of molelcules
Total (without water)9,3041
Polymers9,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: thermal hysteresis protein


Theoretical massNumber of molelcules
Total (without water)9,3041
Polymers9,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: thermal hysteresis protein


Theoretical massNumber of molelcules
Total (without water)9,3041
Polymers9,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: thermal hysteresis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5293
Polymers9,3041
Non-polymers2252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
C: thermal hysteresis protein
D: thermal hysteresis protein
hetero molecules

A: thermal hysteresis protein
B: thermal hysteresis protein


Theoretical massNumber of molelcules
Total (without water)37,4406
Polymers37,2154
Non-polymers2252
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z+1/21
Buried area3490 Å2
ΔGint-38 kcal/mol
Surface area14940 Å2
MethodPISA
6
C: thermal hysteresis protein
D: thermal hysteresis protein
hetero molecules

A: thermal hysteresis protein
B: thermal hysteresis protein


Theoretical massNumber of molelcules
Total (without water)37,4406
Polymers37,2154
Non-polymers2252
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_654x-y+1,x,z-1/61
Buried area3640 Å2
ΔGint-42 kcal/mol
Surface area14790 Å2
MethodPISA
7
C: thermal hysteresis protein
D: thermal hysteresis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8324
Polymers18,6082
Non-polymers2252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-15 kcal/mol
Surface area7970 Å2
MethodPISA
8
A: thermal hysteresis protein
B: thermal hysteresis protein


Theoretical massNumber of molelcules
Total (without water)18,6082
Polymers18,6082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-14 kcal/mol
Surface area7990 Å2
MethodPISA
9
D: thermal hysteresis protein
hetero molecules

B: thermal hysteresis protein


Theoretical massNumber of molelcules
Total (without water)18,8324
Polymers18,6082
Non-polymers2252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z+1/21
Buried area1230 Å2
ΔGint-20 kcal/mol
Surface area8130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.400, 128.400, 68.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
thermal hysteresis protein / antifreeze protein isoform 337


Mass: 9303.827 Da / Num. of mol.: 4 / Mutation: Y33F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Choristoneura fumiferana (eastern spruce budworm)
Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9GTP0
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 4.37 Å3/Da / Density % sol: 71.83 %
Crystal growTemperature: 318 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium dihydrogen phosphate, TRIS, cadmium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 318K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.0 Mammonium dihydrogen phosphate1reservoir
250 mMTris-HCl1reservoirpH7.5
32 mM1reservoirCdCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 9, 2000 / Details: mirrors
RadiationMonochromator: MaxFlux mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→46.79 Å / Num. all: 30101 / Num. obs: 30101 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 48 Å2 / Limit h max: 49 / Limit h min: 1 / Limit k max: 48 / Limit k min: 1 / Limit l max: 29 / Limit l min: 0 / Observed criterion F max: 1159299.7 / Observed criterion F min: 0.71
Reflection shellResolution: 2.25→2.33 Å / % possible all: 96.5
Reflection
*PLUS
Num. obs: 30575 / Num. measured all: 709616 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 96.9 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassificationNB
CNS1refinement
XDSdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAS / Resolution: 2.3→46.79 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2794 9.9 %random
Rwork0.223 ---
all0.227 28119 --
obs0.227 28119 98.2 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 79.123 Å2 / ksol: 0.398034 e/Å3
Displacement parametersBiso max: 133.98 Å2 / Biso mean: 42.64 Å2 / Biso min: 8.75 Å2
Baniso -1Baniso -2Baniso -3
1-6.84 Å20.65 Å20 Å2
2--6.84 Å20 Å2
3----13.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.31 Å
Luzzati d res high-2.3
Refinement stepCycle: LAST / Resolution: 2.3→46.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2460 0 2 181 2643
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg30.1
X-RAY DIFFRACTIONx_torsion_impr_deg0.8
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.3-2.40.3243429.60.31830660.0173559340895.7
2.4-2.530.2933569.90.29630930.0163583344996.3
2.53-2.690.2513339.30.2531670.0143570350098
2.69-2.90.2363489.80.23331430.0133562349198
2.9-3.190.2353319.30.22832010.0133575353298.8
3.19-3.650.243361100.23832060.0133595356799.2
3.65-4.60.2023519.70.19732270.0113603357899.3
4.6-46.790.20637210.10.20932830.0113676365599.4
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ity.parity.top
X-RAY DIFFRACTION4ion.paramion.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg

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