9cbe

Structure of a type III antifreeze protein isoform HPLC12 re-refined using standard protocols

Method: X-RAY DIFFRACTION D_max: 41.6 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Type-3 ice-structuring protein HPLC 12

Zoarces americanus

UniProt P19614

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–63	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：PROTEIN WAS CRYSTALLIZED IN 50-55% AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4-4.5	Resolution 1.90 Å R-free 0.189

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9CBE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AME CRYSTAL STRUCTURE OF TYPE III ANTIFREEZE PROTEIN AT 4 C Deposited 1997-06-13	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–63（63 aa）	Mutation：INS(0), P64A, P65A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；277 K；53% AMMONIUM SULFATE 100 MM SODIUM ACETATE PH 4.5 CRYSTALLIZED AT 4 DEGREES C, temperature 277K	Resolution 1.65 Å R-free 0.282
1B7I TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 K61R Deposited 1999-01-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：K61R, P64A, P65A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.65 Å R-free 0.238
1B7J TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 V20A Deposited 1999-01-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：V20A, P64A, P65A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.65 Å R-free 0.215
1B7K TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 R47H Deposited 1999-01-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：R47H, P64A, P65A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.50 Å R-free 0.256
1EKL TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 E35K Deposited 1999-01-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：E35K, P64A, P65A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.65 Å R-free 0.223
1GZI CRYSTAL STRUCTURE OF TYPE III ANTIFREEZE PROTEIN FROM OCEAN POUT, AT 1.8 ANGSTROM RESOLUTION Deposited 1996-10-25	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–66（66 aa）	Mutation：P64A, P65A, DEL(A66)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；50% AMMONIUM SULFATE, 0.1M SODIUM ACETATE, PH 5.6	Resolution 1.80 Å R-free 0.233
1HG7 High resolution structure of HPLC-12 type III antifreeze protein from Ocean Pout Macrozoarces americanus Deposited 2000-12-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：YES	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；50% AMMONIUM SULFATE, 0.1M SODIUM ACETATE, PH 4.6	Resolution 1.15 Å R-free 0.169
1JAB TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 T18S Deposited 1999-01-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：T18S, P64A, P65A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.65 Å R-free 0.217
1KDE NORTH-ATLANTIC OCEAN POUT ANTIFREEZE PROTEIN TYPE III ISOFORM HPLC12 MUTANT, NMR, 22 STRUCTURES Deposited 1996-07-08	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：INS(M0), P64A, P65A, INS(K66, D67, E68, L69)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.6；298 K	Resolution not provided
1KDF NORTH-ATLANTIC OCEAN POUT ANTIFREEZE PROTEIN TYPE III ISOFORM HPLC12 MUTANT, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-07-08	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：INS(M0), P64A, P65A, INS(K66, D67, E68, L69)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.6；298 K	Resolution not provided
1MSI STRUCTURE OF ANTIFREEZE GLYCOPROTEIN QAE(HPLC 12) Deposited 1996-10-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–66（65 aa）	Mutation：P64A, P65A	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.25 Å R-free 0.225
1MSJ TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 T15V Deposited 1999-01-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：T15V, P64A, P65A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.30 Å R-free 0.310
2AME TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 N14Q Deposited 1999-01-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：N14Q, P64A, P65A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.00 Å R-free 0.261
2JIA TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 K61I Deposited 1999-01-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：K61I, P64A, P65A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.60 Å R-free 0.259
2MSI TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 Deposited 1997-09-16	Different construct Different mutation/modification Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–63（62 aa）	Mutation：A16M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions PROTEIN WAS CRYSTALLIZED IN 50-55% AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4-4.5	Resolution 1.90 Å R-free 0.261
2MSJ TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 N46S Deposited 1999-01-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：N46S, P64A, P65A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.90 Å R-free 0.326
2SPG TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 T15S Deposited 1999-01-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：T15S, P64A, P65A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.75 Å R-free 0.249
3AME TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 Q9TQ44T Deposited 1999-01-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：Q9T, Q44T, P64A, P65A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.30 Å R-free 0.299
3MSI TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 Deposited 1997-09-17	Different construct Different mutation/modification Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–63（62 aa）	Mutation：A16H	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions PROTEIN WAS CRYSTALLIZED IN 50-55% AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4-4.5	Resolution 1.43 Å R-free 0.287
3QF6 Neutron structure of type-III Antifreeze Protein allows the reconstruction of AFP-ice interface Deposited 2011-01-21	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–66（66 aa）	Not recorded	No recorded non-water small molecule	NEUTRON DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；285 K；2.2M ammonium sulfate, 9% d8-glycerol, 50mM sodium acetate, pD 5.2, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 285K	Resolution 1.85 Å R-free 0.216
4AME TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 T18A Deposited 1999-01-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：T18A, P64A, P65A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.05 Å R-free 0.238
4MSI TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 Deposited 1997-09-16	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–63（62 aa）	Mutation：A16T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；PROTEIN WAS CRYSTALLIZED IN 50-55% AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4-4.5	Resolution 1.60 Å R-free 0.199
4NY6 Neutron structure of leucine and valine methyl protonated type III antifreeze Deposited 2013-12-10	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–63（63 aa）	Not recorded	No recorded non-water small molecule	Experimental method not declared X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.2；285 K；10mg/ml protein in 50 mM sodium acetate pD 5.2. Drops containing 20 ml protein solution and 30 ml precipitant buffer (2.1 M ammonium sulfate, 9% d8-glycerol) were equilibrated against 1 ml precipitant buffer in the reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 285K	Resolution not provided
5C7R Revealing surface waters on an antifreeze protein by fusion protein crystallography Deposited 2015-06-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–63（63 aa） Fragment：UNP P0AEY0 residues 27-384, UNP P19614 residues 1-63	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；298 K；1.75 M (NH4)2SO4, 100 mM NaOAC (pH 4.4)	Resolution 1.94 Å R-free 0.234
5C7R Revealing surface waters on an antifreeze protein by fusion protein crystallography Deposited 2015-06-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–63（63 aa） Fragment：UNP P0AEY0 residues 27-384, UNP P19614 residues 1-63	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；298 K；1.75 M (NH4)2SO4, 100 mM NaOAC (pH 4.4)	Resolution 1.94 Å R-free 0.234
5MSI TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 Deposited 1997-09-17	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–63（62 aa）	Mutation：A16C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；PROTEIN WAS CRYSTALLIZED IN 50-55% AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4-4.5	Resolution 1.60 Å R-free 0.199
6AME TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 M21A Deposited 1999-01-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：M21A, P64A, P65A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.10 Å R-free 0.237
6MSI TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 Deposited 1997-09-17	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–63（62 aa）	Mutation：A16R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；PROTEIN WAS CRYSTALLIZED IN 50-55% AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4-4.5	Resolution 1.65 Å
7AME TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 T15A Deposited 1999-01-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：T15A, P64A, P65A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.70 Å R-free 0.237
7MSI TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 Deposited 1997-09-17	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–63（62 aa）	Mutation：A16Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；PROTEIN WAS CRYSTALLIZED IN 50-55% AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4-4.5	Resolution 1.70 Å R-free 0.207
7Q3V Re-refined structure of a type III antifreeze protein isoform HPLC 12 Deposited 2021-10-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–63（62 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50-55% AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4-4.5	Resolution 1.90 Å R-free 0.194
7Q3V Re-refined structure of a type III antifreeze protein isoform HPLC 12 Deposited 2021-10-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–63（62 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50-55% AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4-4.5	Resolution 1.90 Å R-free 0.194
7Q3V Re-refined structure of a type III antifreeze protein isoform HPLC 12 Deposited 2021-10-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2–63（62 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50-55% AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4-4.5	Resolution 1.90 Å R-free 0.194
7Q3V Re-refined structure of a type III antifreeze protein isoform HPLC 12 Deposited 2021-10-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 2–63（62 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50-55% AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4-4.5	Resolution 1.90 Å R-free 0.194
8AME TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 N14SA16H Deposited 1999-01-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：N14S, A16H, P64A, P65A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.90 Å R-free 0.260
8MSI TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 N14SQ44T Deposited 1999-01-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：N14S, Q44T, P64A, P65A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.60 Å R-free 0.268
9AME TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 S42G Deposited 1999-01-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：S42G, P64A, P65A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.80 Å R-free 0.269
9MSI TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 T18N Deposited 1999-01-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Mutation：T18N, P64A, P65A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.60 Å R-free 0.244

34 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ANP12_ZOAAM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–64； UniProt 1–63

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9cbe
Deposition date deposition_date	2024-06-19
最后修订 last_revision	2024-07-17
Structure title title	Structure of a type III antifreeze protein isoform HPLC12 re-refined using standard protocols
Keywords keywords	Re-refinement, ANTIFREEZE PROTEIN; ANTIFREEZE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	12.13 Å
Radius of gyration Rg (electron density) rg_electron	10.79 Å
Forward intensity I(0) i0	1097790.00
Molecular weight molecular_weight	7096.0 kDa
Excluded volume excluded_volume	8985 Å³
Envelope volume envelope_volume	9532 Å³
Hydration-shell volume shell_volume	7858 Å³
Envelope diameter envelope_diameter	39.1 Å
Shell Rg shell_rg	16.08 Å
Envelope Rg envelope_rg	11.11 Å
Shape Rg shape_rg	10.76 Å
Total Rg total_rg	12.30 Å
Total atoms total_atoms	491
Residues n_residues	66
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	41.6 Å
Rg (real space) rg_real	12.07 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	1.0980e+06
I(0) uncertainty (real space) i0_real_error	1.1410e+04
Rg (reciprocal space) rg_reciprocal	12.07 Å
I(0) (reciprocal space) i0_reciprocal	1098000.0000
Solution quality estimate total_estimate	0.8508
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.3 Å
Skewness Skewness skewness	0.224
Kurtosis Kurtosis kurtosis	-0.087
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	239400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.698; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.962

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (2)

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Unit-cell length a length_a	33.270 Å
Unit-cell length b length_b	39.890 Å
Unit-cell length c length_c	44.540 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1522
R_work r_work	0.1500
R_free r_free	0.1891

Description description	Type-3 ice-structuring protein HPLC 12
Molecular weight formula_weight	7099.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	534

Structure of a type III antifreeze protein isoform HPLC12 re-refined using standard protocols

1. Protein Identity and Related Structures Protein Identity & Related Structures

Type-3 ice-structuring protein HPLC 12

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Zoarces americanus
通用名 common_name	ocean pout
NCBI Class编号 ncbi_taxonomy_id	8199
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	39

fit	/app/data/saxs_computation/cb/9cbe/9cbe.fit
pddf	/app/data/pr_computation/cb/9cbe/9cbe.pr.out
profile	/app/data/saxs_computation/cb/9cbe/9cbe.dat