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- PDB-1k6f: Crystal Structure of the Collagen Triple Helix Model [(Pro-Pro-Gl... -

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Basic information

Entry
Database: PDB / ID: 1k6f
TitleCrystal Structure of the Collagen Triple Helix Model [(Pro-Pro-Gly)10]3
Componentscollagen triple helix
KeywordsSTRUCTURAL PROTEIN / collagen stability / puckering / amino acid preferences / triple helix
Function / homologySaimiri transformation-associated protein / extracellular matrix structural constituent conferring tensile strength / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / extracellular matrix organization / extracellular space / membrane / Saimiri transformation-associated protein
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / ARP/WARP / Resolution: 1.3 Å
AuthorsBerisio, R. / Vitagliano, L. / Mazzarella, L. / Zagari, A.
Citation
Journal: Protein Sci. / Year: 2002
Title: Crystal structure of the collagen triple helix model [(Pro-Pro-Gly)(10)](3)
Authors: Berisio, R. / Vitagliano, L. / Mazzarella, L. / Zagari, A.
#1: Journal: Protein Sci. / Year: 2001
Title: Preferred proline puckering in cis and trans peptide groups: implications for collagen stability
Authors: Vitagliano, L. / Berisio, R. / Mastrangelo, A. / Mazzarella, L. / Zagari, A.
#2: Journal: Biopolymers / Year: 2001
Title: Structural Bases of Collagen Stabilization Induced by Proline Hydroxylation
Authors: Vitagliano, L. / Berisio, R. / Mazzarella, L. / Zagari, A.
#3: Journal: Biopolymers / Year: 2001
Title: Crystal Structure of a Collagen-Like Polypeptide with Repeating Sequence Pro-Hyp-Gly at 1.4 A Resolution: Implications for Collagen Hydration
Authors: Berisio, R. / Vitagliano, L. / Mazzarella, L. / Zagari, A.
History
DepositionOct 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Remark 999SEQUENCE An appropriate sequence database reference was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: collagen triple helix
B: collagen triple helix
C: collagen triple helix
D: collagen triple helix
E: collagen triple helix
F: collagen triple helix


Theoretical massNumber of molelcules
Total (without water)15,1856
Polymers15,1856
Non-polymers00
Water6,287349
1
A: collagen triple helix
B: collagen triple helix
C: collagen triple helix


Theoretical massNumber of molelcules
Total (without water)7,5923
Polymers7,5923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-31 kcal/mol
Surface area4720 Å2
MethodPISA
2
D: collagen triple helix
E: collagen triple helix
F: collagen triple helix


Theoretical massNumber of molelcules
Total (without water)7,5923
Polymers7,5923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-31 kcal/mol
Surface area4720 Å2
MethodPISA
3
A: collagen triple helix
B: collagen triple helix
C: collagen triple helix

D: collagen triple helix
E: collagen triple helix
F: collagen triple helix


Theoretical massNumber of molelcules
Total (without water)15,1856
Polymers15,1856
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x+1/2,-y+2,z+1/21
Buried area10610 Å2
ΔGint-79 kcal/mol
Surface area8410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.907, 26.357, 182.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide
collagen triple helix


Mass: 2530.828 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. / References: UniProt: Q80BK4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.11 Å3/Da / Density % sol: 41.82 %
Crystal growTemperature: 294 K
Method: microdialysis carried out in microgravity conditions
pH: 5.6
Details: HAc/NaAc, pH 5.6, microdialysis carried out in microgravity conditions, temperature 21K
Crystal grow
*PLUS
Method: microgravity conditions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.0 mg/mlpolypeptide11
20.05 Macetic acid11
30.22 Msodium acetate11
410 %(v/v)PEG40011

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12941
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONELETTRA 5.2R10.9
SYNCHROTRONEMBL/DESY, HAMBURG BW7B20.87
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.871
ReflectionNum. all: 29431 / Num. obs: 23121
Reflection
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 15 Å / % possible obs: 88.3 % / Rmerge(I) obs: 0.09

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Processing

Software
NameClassification
ARP/wARPmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: ARP/WARP / Resolution: 1.3→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.297 1152 random
Rwork0.181 --
all0.226 29431 -
obs0.185 23121 -
Refinement stepCycle: LAST / Resolution: 1.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1056 0 0 352 1408
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.026
X-RAY DIFFRACTIONc_angle_d0.045
LS refinement shellResolution: 1.3→1.33 Å
RfactorNum. reflection
Rfree0.2978 1152
Rwork0.1813 -
obs-23121
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 15 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_plane_restr0.056

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