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- PDB-1cgd: HYDRATION STRUCTURE OF A COLLAGEN PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1cgd
TitleHYDRATION STRUCTURE OF A COLLAGEN PEPTIDE
ComponentsCOLLAGEN-LIKE PEPTIDE
KeywordsCOLLAGEN / COLLAGEN HYDRATION / HYDROXYPROLINE / CONNECTIVE TISSUE / EXTRACELLULAR MATRIX
Function / homologyACETIC ACID
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsBella, J. / Brodsky, B. / Berman, H.M.
Citation
Journal: Structure / Year: 1995
Title: Hydration structure of a collagen peptide.
Authors: Bella, J. / Brodsky, B. / Berman, H.M.
#1: Journal: Science / Year: 1994
Title: Crystal and Molecular Structure of a Collagen-Like Peptide at 1.9 A Resolution
Authors: Bella, J. / Eaton, M. / Brodsky, B. / Berman, H.M.
History
DepositionJun 9, 1995Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COLLAGEN-LIKE PEPTIDE
B: COLLAGEN-LIKE PEPTIDE
C: COLLAGEN-LIKE PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,53510
Polymers8,1153
Non-polymers4207
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-30 kcal/mol
Surface area5090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.460, 14.057, 25.308
Angle α, β, γ (deg.)90.00, 95.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide COLLAGEN-LIKE PEPTIDE / (PRO-HYP-GLY)4 PRO-HYP-ALA (PRO-HYP-GLY)5


Mass: 2704.854 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: HYDRATION ANALYSIS
#2: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHYDROGEN BONDS BETWEEN PEPTIDE CHAINS FOLLOW THE RICH AND CRICK MODEL II FOR COLLAGEN. AT THE ...HYDROGEN BONDS BETWEEN PEPTIDE CHAINS FOLLOW THE RICH AND CRICK MODEL II FOR COLLAGEN. AT THE ALANINE SUBSTITUTION FOUR INTERSTITIAL WATER MOLECULES INTERCONNECT THE PEPTIDE CHAINS THROUGH GLY - H2O - PRO HYDROGEN-BONDED BRIDGES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.73 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Bella, J., (1994) Science, 266, 75.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14.0-6.0 mg/mlpeptide1drop
210 %acetic acid1drop
39.5 %PEG4001drop
40.1 %sodium azide1drop
519 %PEG4001reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→86.7 Å / Num. obs: 5595 / % possible obs: 99.9 % / Observed criterion σ(I): 0

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Processing

Software
NameClassification
X-PLORrefinement
MOLENdata reduction
RefinementResolution: 1.85→12.5 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.172 --
obs0.172 4020 72.1 %
Displacement parametersBiso mean: 11 Å2
Refinement stepCycle: LAST / Resolution: 1.85→12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms576 0 28 141 745
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.53
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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