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- PDB-1g9w: STRUCTURAL BASIS OF COLLAGEN STABILIZATION INDUCED BY PROLINE HYD... -

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Basic information

Entry
Database: PDB / ID: 1g9w
TitleSTRUCTURAL BASIS OF COLLAGEN STABILIZATION INDUCED BY PROLINE HYDROXYLATION
Components(COLLAGEN-LIKE PEPTIDE) x 2
KeywordsSTRUCTURAL PROTEIN / COLLAGEN / EXTRACELLULAR MATRIX
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.3 Å
AuthorsVitagliano, L. / Berisio, R. / Mazzarella, L. / Zagari, A.
Citation
Journal: Biopolymers / Year: 2001
Title: Structural bases of collagen stabilization induced by proline hydroxylation.
Authors: Vitagliano, L. / Berisio, R. / Mazzarella, L. / Zagari, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Effects of microgravity on the crystal quality of a collagen-like polypeptide
Authors: Berisio, R. / Vitagliano, L. / Sorrentino, G. / Carotenuto, L. / Piccolo, C. / Mazzarella, L. / Zagari, A.
#2: Journal: J.Mol.Biol. / Year: 1998
Title: X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A COLLAGEN-LIKE PEPTIDE WITH THE REPEATING SEQUENCE (PRO-PRO-GLY)
Authors: Kramer, R.Z. / Vitagliano, L. / Bella, J. / Berisio, R. / Mazzarella, L. / Brodsky, B. / Zagari, A. / Berman, H.M.
History
DepositionNov 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 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-LIKE PEPTIDE
B: COLLAGEN-LIKE PEPTIDE
C: COLLAGEN-LIKE PEPTIDE


Theoretical massNumber of molelcules
Total (without water)1,8133
Polymers1,8133
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-7 kcal/mol
Surface area1540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.887, 26.340, 20.288
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE 21 RESIDUE ASYMMETRIC UNIT CORRESPONDS TO ONE TRIPLE-HELICAL REPEAT AND IS SMALLER THAN THE ENTIRE 90 RESIDUE PEPTIDE. THE RESULT IS A POLYMER-LIKE STRUCTURE WITH NO DEFINED ENDS. THE POLYMER STRUCTURE IS FORMED BY CONTINUATION OF THE CHAINS USING THE SYMMETRY-RELATED MOLECULES ALONG THE HELICAL AXIS. THE TVECT RECORD BELOW PRESENTS THE TRANSLATION THAT WILL GENERATE THE POLYMER. NOTE: THEREFORE, CLOSE CONTACTS BETWEEN SYMMETRY-RELATED MOLECULES ARE INTENTIONAL AND NECESSARY. INTERCHAIN HYDROGEN BONDING AT THE END OF CHAINS ALSO UTILIZES SYMMETRY-RELATED MOLECULES. THE ENTIRE 30 RESIDUE LONG PEPTIDE CAN BE GENERATED FROM THE SUBMITTED ASYMMETRIC UNIT BY APPLYING THE FOLLOWING TRANSLATIONS (USING FRACTIONAL COORDINATES): CHAIN A: TRANSLATE RESIDUES 1 - 9 BY (0 0 1), (0 0 2), AND (0 0 3) AND RESIDUES 7 - 9 BY (0 0 4). CHAIN B: TRANSLATE RESIDUES 31 - 36 BY (0 0 1), (0 0 2), AND (0 0 3). CHAIN C: TRANSLATE RESIDUES 61 - 66 BY (0 0 1), (0 0 2), AND (0 0 3) AND RESIDUES 64 - 66 BY (004). THIS WILL RESULT IN A MOLECULE WITH A TOTAL OF 90 RESIDUES, 30 IN EACH CHAIN.

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Components

#1: Protein/peptide COLLAGEN-LIKE PEPTIDE


Mass: 771.859 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein/peptide COLLAGEN-LIKE PEPTIDE


Mass: 520.578 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHYDROGEN BONDS BETWEEN PEPTIDE CHAINS FOLLOW THE RICH AND CRICK MODEL II FOR COLLAGEN.
Sequence detailsFOR EACH CHAIN, RESIDUE NUMBERING CORRESPONDS TO THE ENTIRE MOLECULE RATHER THAN THE SHORTER ASYMMETRIC UNIT.

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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: 1.97 Å3/Da / Density % sol: 37.43 %
Crystal growTemperature: 293 K / Method: dialysis
Details: SODIUM ACETATE, ACETIC ACID, DIALYSIS, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Kramer, R.Z., (1998) J.Mol.Biol., 280, 623.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlpeptide1drop
25 %(v/v)aqueous acetic acid1drop
30.1 Macetate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.004
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.004 Å / Relative weight: 1
ReflectionResolution: 1.3→15 Å / Num. obs: 3448 / % possible obs: 89 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.042
Reflection shellResolution: 1.3→1.33 Å / Rmerge(I) obs: 0.093 / % possible all: 66.4
Reflection shell
*PLUS
% possible obs: 66.4 %

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: PDB1A3J.ENT

Resolution: 1.3→10 Å / Num. parameters: 147 / Num. restraintsaints: 179 / Cross valid method: THROUGHOUT / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
Details: DUE TO THE QUASI-INFINITE NATURE OF THE TRIPLE HELIX, DURING REFINEMENT COVALENT BONDS ARE NECESSARY TO JOIN THE MOLECULE WITH ITS SYMMETRY MATES BOTH ABOVE IT AND BELOW IT ALONG THE HELICAL ...Details: DUE TO THE QUASI-INFINITE NATURE OF THE TRIPLE HELIX, DURING REFINEMENT COVALENT BONDS ARE NECESSARY TO JOIN THE MOLECULE WITH ITS SYMMETRY MATES BOTH ABOVE IT AND BELOW IT ALONG THE HELICAL AXIS AND TIGHT REFINEMENT CONSTRAINTS WERE MAINTAINED. THE UNIT CELL AXES WERE CHOSEN TO COINCIDE WITH A PREVIOUS STRUCTURE DETERMINATION (OKUYAMA 1981) OF THIS PEPTIDE.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 -20 %RANDOM
obs0.147 -89 %-
all-320 --
Refine analyzeOccupancy sum non hydrogen: 162
Refinement stepCycle: LAST / Resolution: 1.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms126 0 0 36 162
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_d0.026
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_plane_restr0.03

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