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- PDB-1cag: CRYSTAL AND MOLECULAR STRUCTURE OF A COLLAGEN-LIKE PEPTIDE AT 1.9... -

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Basic information

Entry
Database: PDB / ID: 1cag
TitleCRYSTAL AND MOLECULAR STRUCTURE OF A COLLAGEN-LIKE PEPTIDE AT 1.9 ANGSTROM RESOLUTION
ComponentsCOLLAGEN-LIKE PEPTIDE
KeywordsCOLLAGEN
Function / homologyACETIC ACID
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsBella, J. / Eaton, M. / Brodsky, B. / Berman, H.M.
CitationJournal: 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
DepositionMar 29, 1994Processing site: BNL
Revision 1.0Nov 1, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)8,4759
Polymers8,1153
Non-polymers3606
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-30 kcal/mol
Surface area4960 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
Atom site foot note1: CIS HYDROXYPROLINE - HYP B 32 / 2: CIS HYDROXYPROLINE - HYP C 62

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Components

#1: Protein/peptide COLLAGEN-LIKE PEPTIDE


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


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHYDROGEN BONDS BETWEEN PEPTIDE CHAINS FOLLOW THE RICH AND CRICK MODEL II FOR COLLAGEN. THESE HAVE ...HYDROGEN BONDS BETWEEN PEPTIDE CHAINS FOLLOW THE RICH AND CRICK MODEL II FOR COLLAGEN. THESE HAVE BEEN PRESENTED ON *CONECT* RECORDS IN THIS ENTRY. AT THE ALANINE SUBSTITUTION FOUR INTERSTITIAL WATER MOLECULES INTERCONNECT THE PEPTIDE CHAINS THROUGH GLY - H2O - PRO HYDROGEN-BONDED BRIDGES. THESE ALSO ARE PRESENTED ON *CONECT* RECORDS.

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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
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

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.85 Å / Num. obs: 5595 / % possible obs: 100 % / Observed criterion σ(I): 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.85→8 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.197 -
obs0.197 3393
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms565 0 0 109 674
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg2.3
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_d1.7
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.197 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.3

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