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- PDB-3a0a: Structure of (PPG)4-OPG-(PPG)4, monoclinic, twinned crystal -

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Basic information

Entry
Database: PDB / ID: 3a0a
TitleStructure of (PPG)4-OPG-(PPG)4, monoclinic, twinned crystal
Componentscollagen-like peptide
KeywordsSTRUCTURAL PROTEIN / collagen / triple helix / model peptide
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsOkuyama, K. / Morimoto, T. / Hongo, C. / Katagiri, A. / Tanaka, Y. / Nishino, N.
CitationJournal: To be Published
Title: Crystal structure of (PPG)4-OPG-(PPG)4
Authors: Okuyama, K. / Morimoto, T. / Hongo, C. / Tanaka, Y. / Nishino, N.
History
DepositionMar 13, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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

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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)13,7736
Polymers13,7736
Non-polymers00
Water4,107228
1
A: collagen-like peptide
B: collagen-like peptide
C: collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)6,8873
Polymers6,8873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-25 kcal/mol
Surface area3630 Å2
MethodPISA
2
D: collagen-like peptide
E: collagen-like peptide
F: collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)6,8873
Polymers6,8873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-24 kcal/mol
Surface area3550 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-63 kcal/mol
Surface area6290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.007, 26.538, 80.146
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
collagen-like peptide


Mass: 2295.547 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.: 228 / 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: 2.01 Å3/Da / Density % sol: 38.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 10%(v/v) acetic acid, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 21, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.445
ReflectionResolution: 1.36→24.75 Å / Num. obs: 23900 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.08
Reflection shellResolution: 1.36→1.41 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.29 / % possible all: 98

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Processing

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

2cuo


Resolution: 1.36→24.74 Å / Num. parameters: 9391 / Num. restraintsaints: 11722 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: THE STRUCTURE WAS REFINED UNDER THE TWINNING OPERATOR (H,-K,-L) AND THE TWINNING FRACTION 0.445 USING THE TWINNED DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1157 -RANDOM
Rwork0.14 ---
obs-23170 92.1 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1043
Refinement stepCycle: LAST / Resolution: 1.36→24.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms815 0 0 228 1043
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.028
X-RAY DIFFRACTIONs_zero_chiral_vol0.062
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.007
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.058
X-RAY DIFFRACTIONs_approx_iso_adps0.096
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.36-1.410.221X-RAY DIFFRACTION23516
1.41-1.470.173X-RAY DIFFRACTION21096
1.47-1.530.148X-RAY DIFFRACTION22406
1.53-1.610.138X-RAY DIFFRACTION21666
1.61-1.710.132X-RAY DIFFRACTION21526
1.71-1.850.117X-RAY DIFFRACTION22406

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