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- PDB-1itt: Average Crystal Structure of (Pro-Pro-Gly)9 at 1.0 angstroms Reso... -

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Basic information

Entry
Database: PDB / ID: 1itt
TitleAverage Crystal Structure of (Pro-Pro-Gly)9 at 1.0 angstroms Resolution
Components(COLLAGEN TRIPLE HELIX) x 3
KeywordsSTRUCTURAL PROTEIN / collagen / triple helix / Pro-Pro-Gly / single crystal
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsHongo, C. / Nagarajan, V. / Noguchi, K. / Kamitori, S. / Okuyama, K. / Tanaka, Y. / Nishino, N.
CitationJournal: Plym.J. / Year: 2001
Title: Average Crystal Structure of (Pro-Pro-Gly)9 at 1.0 angstroms Resolution
Authors: Hongo, C. / Nagarajan, V. / Noguchi, K. / Kamitori, S. / Okuyama, K. / Tanaka, Y. / Nishino, N.
History
DepositionFeb 3, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 25, 2013Group: Derived calculations
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COLLAGEN TRIPLE HELIX
B: COLLAGEN TRIPLE HELIX
C: COLLAGEN TRIPLE HELIX


Theoretical massNumber of molelcules
Total (without water)1,8133
Polymers1,8133
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-7 kcal/mol
Surface area1440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.821, 26.333, 20.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE ENTIRE 27 RESIDUE LONG PEPTIDE CAN BE GENERATED FROM THE SUBMITTED ASYMMETRIC UNIT BY APPLYING THE FOLLOWING TRANSLATIONS (USING FRACTIONAL COORDINATES): CHAIN A: TRANSLATE RESIDUES 2 - 7 BY (0 0 1), AND RESIDUES 1-7 BY (002), (003), (004) AND RESIDUE 1 BY (005). CHAIN B: TRANSLATE RESIDUES 33-37 BY (0 0 1), AND RESIDUES 31-37 BY (002), (003), (004) AND RESIDUE 31-32 BY (005). CHAIN C: TRANSLATE RESIDUES 64-67 BY (0 0 1), AND RESIDUES 61-67 BY (002), (003), (004). THIS WILL RESULT IN A MOLECULE WITH A TOTAL OF 81 RESIDUES, 27 IN EACH CHAIN.

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Components

#1: Protein/peptide COLLAGEN TRIPLE HELIX


Mass: 577.630 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in collagens.
#2: Protein/peptide COLLAGEN TRIPLE HELIX


Mass: 617.693 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in collagens.
#3: Protein/peptide COLLAGEN TRIPLE HELIX


Mass: 617.693 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in collagens.
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.96 Å3/Da / Density % sol: 37.13 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop
Details: PEG400, acetic acid, sodium azide, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER / Date: May 18, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1→8 Å / Num. all: 6129 / Num. obs: 2922 / Observed criterion σ(F): 1

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Processing

Software
NameClassification
TEXSANdata collection
teXsandata reduction
X-PLORmodel building
SHELXL-97refinement
TEXSANdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The structural model for collagen proposed by Okuyama (1981)

Resolution: 1→8 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.294 292 random
Rwork0.222 --
all-2922 -
obs-2922 -
Refinement stepCycle: LAST / Resolution: 1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms126 0 0 34 160
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.02

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