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- PDB-3abn: Crystal structure of (Pro-Pro-Gly)4-Hyp-Asp-Gly-(Pro-Pro-Gly)4 at... -

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Basic information

Entry
Database: PDB / ID: 3abn
TitleCrystal structure of (Pro-Pro-Gly)4-Hyp-Asp-Gly-(Pro-Pro-Gly)4 at 1.02 A
Componentscollagen-like peptide
KeywordsSTRUCTURAL PROTEIN / collagen-helix
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
AuthorsOkuyama, K. / Shimura, M. / Kawaguchi, T. / Noguchi, K. / Mizuno, K. / Bachinger, H.P.
CitationJournal: Biopolymers / Year: 2013
Title: Crystal structure of the collagen model peptide (Pro-Pro-Gly)4 -Hyp-Asp-Gly-(Pro-Pro-Gly)4 at 1.0 angstrom resolution.
Authors: Okuyama, K. / Kawaguchi, T. / Shimura, M. / Noguchi, K. / Mizuno, K. / Bachinger, H.P.
History
DepositionDec 16, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 27, 2013Group: Database references
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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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


Theoretical massNumber of molelcules
Total (without water)6,9413
Polymers6,9413
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-26 kcal/mol
Surface area4170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.590, 21.706, 39.151
Angle α, β, γ (deg.)90.00, 100.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide collagen-like peptide


Mass: 2313.520 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: THIS PEPTIDE WAS CHEMICALLY SYSTHESIZED.
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS SEQUENCE ADOPTS 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: 1.9 Å3/Da / Density % sol: 35.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 15% PEG 4000, 0.05M Ammonium Acetate, 0.05M Sodium Acetate Trihydrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: Feb 18, 2005 / Details: 1.1 M 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: 1.02→22.35 Å / Num. obs: 27010 / % possible obs: 99.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 11.7
Reflection shellResolution: 1.02→1.06 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2687 / % possible all: 99.6

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Processing

Software
NameClassification
HKL-2000data collection
X-PLORmodel building
SHELXL-97refinement
CrystalCleardata reduction
CrystalCleardata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.02→10 Å / Num. parameters: 5737 / Num. restraintsaints: 7108 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.163 1259 -RANDOM
Rwork0.13 ---
all-25349 --
obs-25349 89.3 %-
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 410.44 / Occupancy sum non hydrogen: 625.42
Refinement stepCycle: LAST / Resolution: 1.02→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms465 0 0 164 629
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0393
X-RAY DIFFRACTIONs_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.011
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0.086
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.02-1.060.158X-RAY DIFFRACTION24676
1.06-1.110.146X-RAY DIFFRACTION24176
1.11-1.160.133X-RAY DIFFRACTION23896
1.16-1.220.125X-RAY DIFFRACTION24586
1.22-1.30.13X-RAY DIFFRACTION23566
1.3-1.390.123X-RAY DIFFRACTION23806

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