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- PDB-1ei8: STRUCTURAL CONSEQUENCES OF A DISCONTINUITY IN THE REPEATING TRIPE... -

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Basic information

Entry
Database: PDB / ID: 1ei8
TitleSTRUCTURAL CONSEQUENCES OF A DISCONTINUITY IN THE REPEATING TRIPEPTIDE SEQUENCE OF A COLLAGEN-LIKE TRIPLE-HELICAL PEPTIDE
ComponentsCOLLAGEN-LIKE PEPTIDE (PRO-HYP-GLY)4-PG-(PRO-HYP-GLY)5
KeywordsCONTRACTILE PROTEIN / collagen-like peptide / TRIPLE HELIX
Function / homologyFarmer, isoform A
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBerman, H.M. / Liu, J.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Conformational effects of gly-x-gly interruptions in the collagen triple helix.
Authors: Bella, J. / Liu, J. / Kramer, R. / Brodsky, B. / Berman, H.M.
History
DepositionFeb 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COLLAGEN-LIKE PEPTIDE (PRO-HYP-GLY)4-PG-(PRO-HYP-GLY)5
B: COLLAGEN-LIKE PEPTIDE (PRO-HYP-GLY)4-PG-(PRO-HYP-GLY)5
C: COLLAGEN-LIKE PEPTIDE (PRO-HYP-GLY)4-PG-(PRO-HYP-GLY)5
D: COLLAGEN-LIKE PEPTIDE (PRO-HYP-GLY)4-PG-(PRO-HYP-GLY)5
E: COLLAGEN-LIKE PEPTIDE (PRO-HYP-GLY)4-PG-(PRO-HYP-GLY)5
F: COLLAGEN-LIKE PEPTIDE (PRO-HYP-GLY)4-PG-(PRO-HYP-GLY)5


Theoretical massNumber of molelcules
Total (without water)15,4666
Polymers15,4666
Non-polymers00
Water4,486249
1
A: COLLAGEN-LIKE PEPTIDE (PRO-HYP-GLY)4-PG-(PRO-HYP-GLY)5
B: COLLAGEN-LIKE PEPTIDE (PRO-HYP-GLY)4-PG-(PRO-HYP-GLY)5
C: COLLAGEN-LIKE PEPTIDE (PRO-HYP-GLY)4-PG-(PRO-HYP-GLY)5


Theoretical massNumber of molelcules
Total (without water)7,7333
Polymers7,7333
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-25 kcal/mol
Surface area4660 Å2
MethodPISA
2
D: COLLAGEN-LIKE PEPTIDE (PRO-HYP-GLY)4-PG-(PRO-HYP-GLY)5
E: COLLAGEN-LIKE PEPTIDE (PRO-HYP-GLY)4-PG-(PRO-HYP-GLY)5
F: COLLAGEN-LIKE PEPTIDE (PRO-HYP-GLY)4-PG-(PRO-HYP-GLY)5


Theoretical massNumber of molelcules
Total (without water)7,7333
Polymers7,7333
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-26 kcal/mol
Surface area4810 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11820 Å2
ΔGint-74 kcal/mol
Surface area7470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)14.150, 23.770, 82.210
Angle α, β, γ (deg.)85.86, 85.54, 84.34
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 2577.713 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: This peptide was chemically synthesized. / References: UniProt: Q8T018*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.77 Å3/Da / Density % sol: 30.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 10% acetic acid, 15% PEG400, pH N/A, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.4 mg/mlpeptide1drop
210 %(v/v)acetic acid1drop
315 %(w/v)PEG4001drop
430 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 7, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→27 Å / Num. all: 7146 / Num. obs: 5124 / % possible obs: 71.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14
Reflection shellResolution: 2→2.03 Å / Redundancy: 1 % / Rmerge(I) obs: 0.3 / Num. unique all: 198 / % possible all: 66
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 27 Å
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 66 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2→500 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 533 -random
Rwork0.217 ---
all0.251 7148 --
obs0.251 5124 71.7 %-
Refinement stepCycle: LAST / Resolution: 2→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1078 0 0 249 1327
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.669
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_torsion_deg26.01
X-RAY DIFFRACTIONc_torsion_impr_deg2.357
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 27 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.67

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