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- PDB-3b0s: Crystal Structure of (Gly-Pro-Hyp)9 -

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Basic information

Entry
Database: PDB / ID: 3b0s
TitleCrystal Structure of (Gly-Pro-Hyp)9
Componentscollagen-like peptide
KeywordsSTRUCTURAL PROTEIN / collagen / triple helix
Function / homologySaimiri transformation-associated protein / extracellular matrix structural constituent conferring tensile strength / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / extracellular matrix organization / extracellular space / membrane / Saimiri transformation-associated protein
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsOkuyama, K. / Miyama, K. / Mizuno, K. / Bachinger, H.P.
CitationJournal: Biopolymers / Year: 2012
Title: Crystal structure of (Gly-Pro-Hyp)(9) : Implications for the collagen molecular model.
Authors: Okuyama, K. / Miyama, K. / Mizuno, K. / Bachinger, H.P.
History
DepositionJun 14, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 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)14,5416
Polymers14,5416
Non-polymers00
Water6,467359
1
A: collagen-like peptide
B: collagen-like peptide
C: collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)7,2713
Polymers7,2713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-22 kcal/mol
Surface area4410 Å2
MethodPISA
2
D: collagen-like peptide
E: collagen-like peptide
F: collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)7,2713
Polymers7,2713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-22 kcal/mol
Surface area4110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.310, 26.161, 74.507
Angle α, β, γ (deg.)90.00, 92.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
collagen-like peptide


Mass: 2423.547 Da / Num. of mol.: 6 / Source method: obtained synthetically
Details: This peptide appears most frequently in native collagen.
References: UniProt: Q80BK4*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATES THE E-CHAIN CONSISTS OF TWO CHAINS WITH HALF OCCUPANCIES. THESE TWO CHAINS ARE ...AUTHOR STATES THE E-CHAIN CONSISTS OF TWO CHAINS WITH HALF OCCUPANCIES. THESE TWO CHAINS ARE ASSIGNED WITH ALTERNATE POSISION A AND B, AND HAVE EXACTLY THE SAME ATOMIC COORDINATES PARTIALLY. GLY4 - HYP27 (ALT. A) AND GLY1 - HYP24 (ALT. B) ARE SAME.

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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: 1.96 Å3/Da / Density % sol: 37.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 22% PEG 200, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Oct 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 20281 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 4.9
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 3.4 / Num. unique all: 964 / % possible all: 99.9

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DRT

2drt


Resolution: 1.45→8 Å / Num. parameters: 5605 / Num. restraintsaints: 4729 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2559 389 RANDOM
Rwork0.1695 --
all-8267 -
obs-8267 -
Displacement parametersBiso mean: 13.35 Å2
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1385
Refinement stepCycle: LAST / Resolution: 1.45→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 0 0 359 1389
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.018
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.033
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.004
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.062
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.45-1.520.174X-RAY DIFFRACTION8142
1.52-1.610.149X-RAY DIFFRACTION7822
1.61-1.720.149X-RAY DIFFRACTION8022
1.72-1.850.148X-RAY DIFFRACTION7602
1.85-2.020.137X-RAY DIFFRACTION8022
2.02-2.170.142X-RAY DIFFRACTION8022
2.17-2.350.129X-RAY DIFFRACTION7732
2.35-2.660.131X-RAY DIFFRACTION7772
2.66-3.380.153X-RAY DIFFRACTION7902

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