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- PDB-3a1h: Crystal Structure Analysis of the Collagen-like Peptide, (PPG)4-O... -

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Basic information

Entry
Database: PDB / ID: 3a1h
TitleCrystal Structure Analysis of the Collagen-like Peptide, (PPG)4-OTG-(PPG)4
Componentscollagen-like peptide
KeywordsSTRUCTURAL PROTEIN / collagen helix / host-guest peptide / twinned crystal
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsOkuyama, K. / Miyama, K. / Mizuno, K. / Bachinger, H.P.
CitationJournal: Biopolymers / Year: 2011
Title: Stabilization of triple-helical structures of collagen peptides containing a Hyp-Thr-Gly, Hyp-Val-Gly, or Hyp-Ser-Gly sequence.
Authors: Okuyama, K. / Miyama, K. / Morimoto, T. / Masakiyo, K. / Mizuno, K. / Bachinger, H.P.
History
DepositionApr 3, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references / Refinement description
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)13,7976
Polymers13,7976
Non-polymers00
Water3,999222
1
A: collagen-like peptide
B: collagen-like peptide
C: collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)6,8993
Polymers6,8993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-26 kcal/mol
Surface area3830 Å2
MethodPISA
2
D: collagen-like peptide
E: collagen-like peptide
F: collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)6,8993
Polymers6,8993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-26 kcal/mol
Surface area3790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.990, 26.490, 80.210
Angle α, β, γ (deg.)90.00, 89.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
collagen-like peptide


Mass: 2299.536 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.: 222 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE ADOPTS A TRIPLE-HELICAL STRUCURE 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: 1.99 Å3/Da / Density % sol: 38.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 12.5%(w/v) PEG 400, 0.1M MES buffer, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 29, 2008
RadiationMonochromator: the rotated-inclined double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.44
ReflectionResolution: 1.08→26.5 Å / Num. all: 47303 / Num. obs: 46090 / % possible obs: 97.4 % / Observed criterion σ(I): 3 / Redundancy: 3.26 % / Rmerge(I) obs: 0.076
Reflection shellResolution: 1.08→1.12 Å / Redundancy: 3.33 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4661 / % possible all: 99.1

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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: 1.08→26.5 Å / Num. parameters: 9778 / Num. restraintsaints: 12276 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE STRUCTURE WAS REFINED UNDER THE TWINNING OPERATOR (H,-K,-L) AND TWINNING FRACTION 0.44 USING THE TWINNED DATA.
RfactorNum. reflectionSelection details
Rfree0.185 2279 RANDOM
Rwork0.135 --
all-45529 -
obs-45529 -
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1086
Refinement stepCycle: LAST / Resolution: 1.08→26.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms864 0 0 222 1086
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0366
X-RAY DIFFRACTIONs_zero_chiral_vol0.095
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.073
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.012
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.061
X-RAY DIFFRACTIONs_approx_iso_adps0.085
LS refinement shell
Resolution (Å)Rfactor RworkRefine-ID
1.08-1.120.148X-RAY DIFFRACTION
1.12-1.170.13X-RAY DIFFRACTION
1.17-1.220.12X-RAY DIFFRACTION
1.22-1.280.118X-RAY DIFFRACTION
1.28-1.360.111X-RAY DIFFRACTION
1.36-1.460.115X-RAY DIFFRACTION

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