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- PDB-3a08: Structure of (PPG)4-OOG-(PPG)4, monoclinic, twinned crystal -

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Basic information

Entry
Database: PDB / ID: 3a08
TitleStructure of (PPG)4-OOG-(PPG)4, monoclinic, twinned crystal
Componentscollagen-like peptide
KeywordsSTRUCTURAL PROTEIN / collagen helix / host-guest peptide
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsOkuyama, K. / Morimoto, T. / Wu, G. / Noguchi, K. / Mizuno, K. / Bachinger, H.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Two crystal modifications of (Pro-Pro-Gly)4-Hyp-Hyp-Gly-(Pro-Pro-Gly)4 reveal the puckering preference of Hyp(X) in the Hyp(X):Hyp(Y) and Hyp(X):Pro(Y) stacking pairs in collagen helices.
Authors: Okuyama, K. / Morimoto, T. / Narita, H. / Kawaguchi, T. / Mizuno, K. / Bachinger, H.P. / Wu, G. / Noguchi, K.
History
DepositionMar 6, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 17, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: collagen-like peptide
B: collagen-like peptide
C: collagen-like peptide
D: collagen-like peptide
E: collagen-like peptide
F: collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)13,8696
Polymers13,8696
Non-polymers00
Water4,306239
1
A: collagen-like peptide
B: collagen-like peptide
C: collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)6,9353
Polymers6,9353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-24 kcal/mol
Surface area3760 Å2
MethodPISA
2
D: collagen-like peptide
E: collagen-like peptide
F: collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)6,9353
Polymers6,9353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-26 kcal/mol
Surface area3800 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-64 kcal/mol
Surface area6620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.987, 26.668, 79.843
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
collagen-like peptide


Mass: 2311.547 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: THIS PEPTIDE WAS CHEMICALLY SYSTHESIZED.
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE ADOPTS TRIPLE-HELICAL STRUCTURE SIMILAR TO THE COLLAGEN-HELIX.

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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: 2.13 Å3/Da / Density % sol: 38.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 16.25%(w/v) PEG 1000, 0.05M acetate buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 30, 2004 / Details: 1.1-M-LONG BENT-PLANE MIRROR
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.22→26.6 Å / Num. obs: 32577 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Redundancy: 3.52 % / Rmerge(I) obs: 0.082
Reflection shellResolution: 1.22→1.26 Å / Redundancy: 3.79 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CUO

2cuo


Resolution: 1.22→8 Å / Num. parameters: 9886 / Num. restraintsaints: 13177 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE STRUCTURE WAS ANALYZED AGAINST DETWINNED DIFFRACTION DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1627 -RANDOM
Rwork0.139 ---
obs-32044 92.5 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 793 / Occupancy sum non hydrogen: 1098
Refinement stepCycle: LAST / Resolution: 1.22→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms859 0 0 239 1098
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0311
X-RAY DIFFRACTIONs_zero_chiral_vol0.073
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.061
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.009
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.058
X-RAY DIFFRACTIONs_approx_iso_adps0.103
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.22-1.270.177X-RAY DIFFRACTION30786
1.27-1.320.158X-RAY DIFFRACTION31836
1.32-1.380.147X-RAY DIFFRACTION28866
1.38-1.450.151X-RAY DIFFRACTION30466
1.45-1.540.136X-RAY DIFFRACTION31196
1.54-1.660.128X-RAY DIFFRACTION30186

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