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- PDB-2cuo: Collagen model peptide (PRO-PRO-GLY)9 -

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Basic information

Entry
Database: PDB / ID: 2cuo
TitleCollagen model peptide (PRO-PRO-GLY)9
ComponentsCOLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9
KeywordsSTRUCTURAL PROTEIN / COLLAGEN MODEL PEPTIDE / TRIPLE-HELIX / PUCKERING
Function / homologySaimiri transformation-associated protein / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / membrane / Saimiri transformation-associated protein
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsHongo, C. / Noguchi, K. / Okuyama, K. / Tanaka, Y. / Nishino, N.
CitationJournal: J.Biochem.(Tokyo) / Year: 2005
Title: Repetitive interactions observed in the crystal structure of a collagen-model peptide, [(Pro-Pro-Gly)9]3
Authors: Hongo, C. / Noguchi, K. / Okuyama, K. / Tanaka, Y. / Nishino, N.
History
DepositionMay 27, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9
B: COLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9
C: COLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9
D: COLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9
E: COLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9
F: COLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9


Theoretical massNumber of molelcules
Total (without water)13,6776
Polymers13,6776
Non-polymers00
Water5,981332
1
A: COLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9
B: COLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9
C: COLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9


Theoretical massNumber of molelcules
Total (without water)6,8393
Polymers6,8393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-28 kcal/mol
Surface area4250 Å2
MethodPISA
2
D: COLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9
E: COLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9
F: COLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9


Theoretical massNumber of molelcules
Total (without water)6,8393
Polymers6,8393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-28 kcal/mol
Surface area4270 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9790 Å2
ΔGint-72 kcal/mol
Surface area7540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.946, 26.563, 80.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
COLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9


Mass: 2279.547 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: COLLAGEN MODEL PEPTIDE WAS CHEMICALLY SYSTHESIZED / References: UniProt: Q80BK4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 1.71 Å3/Da / Density % sol: 27.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PEG400, ACETIC ACID, SODIUM AZIDE, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 20, 2001 / Details: 1-M-LONG BENT-CYLINDER MIRROR
RadiationMonochromator: FIXED-EXIT DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.33→25.21 Å / Num. obs: 24336 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 4.8
Reflection shellResolution: 1.33→1.38 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 1.8 / % possible all: 98.3

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Processing

Software
NameClassification
CrystalCleardata collection
CrystalCleardata reduction
SHELXmodel building
SHELXL-97refinement
CrystalCleardata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ITT

1itt


Resolution: 1.33→8 Å / Num. parameters: 9953 / Num. restraintsaints: 12321 / σ(F): 1 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 1185 5.1 %RANDOM
Rwork0.1816 ---
obs0.1839 23020 90.8 %-
all-24205 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 918 / Occupancy sum non hydrogen: 1290
Refinement stepCycle: LAST / Resolution: 1.33→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms958 0 0 332 1290
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.0267
X-RAY DIFFRACTIONs_zero_chiral_vol0.056
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.042
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.045
X-RAY DIFFRACTIONs_approx_iso_adps0.034

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