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- PDB-2d3h: Crystal structures of collagen model peptides (Pro-Pro-Gly)4-Hyp-... -

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Basic information

Entry
Database: PDB / ID: 2d3h
TitleCrystal structures of collagen model peptides (Pro-Pro-Gly)4-Hyp-Hyp-Gly-(Pro-Pro-Gly)4
ComponentsCOLLAGEN MODEL PEPTIDES (PRO-PRO-GLY)4-HYP-HYP-GLY-(PRO-PRO-GLY)4
KeywordsSTRUCTURAL PROTEIN / COLLAGEN / TRIPLE-HELIX / HYDROXYPROLINE
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: 1.22 Å
AuthorsWu, G. / Noguchi, K. / Okuyama, K. / Mizuno, K. / Bachinger, H.P.
CitationJournal: Biopolymers / Year: 2009
Title: High-resolution structures of collagen-like peptides [(Pro-Pro-Gly)(4)-Xaa-Yaa-Gly-(Pro-Pro-Gly)(4)]: Implications for triple-helix hydration and Hyp(X) puckering.
Authors: Okuyama, K. / Hongo, C. / Wu, G. / Mizuno, K. / Noguchi, K. / Ebisuzaki, S. / Tanaka, Y. / Nishino, N. / Bachinger, H.P.
History
DepositionSep 28, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 MODEL PEPTIDES (PRO-PRO-GLY)4-HYP-HYP-GLY-(PRO-PRO-GLY)4
B: COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY)4-HYP-HYP-GLY-(PRO-PRO-GLY)4
C: COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY)4-HYP-HYP-GLY-(PRO-PRO-GLY)4
D: COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY)4-HYP-HYP-GLY-(PRO-PRO-GLY)4
E: COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY)4-HYP-HYP-GLY-(PRO-PRO-GLY)4
F: COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY)4-HYP-HYP-GLY-(PRO-PRO-GLY)4


Theoretical massNumber of molelcules
Total (without water)13,8696
Polymers13,8696
Non-polymers00
Water4,738263
1
A: COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY)4-HYP-HYP-GLY-(PRO-PRO-GLY)4
B: COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY)4-HYP-HYP-GLY-(PRO-PRO-GLY)4
C: COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY)4-HYP-HYP-GLY-(PRO-PRO-GLY)4


Theoretical massNumber of molelcules
Total (without water)6,9353
Polymers6,9353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-26 kcal/mol
Surface area3950 Å2
MethodPISA
2
D: COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY)4-HYP-HYP-GLY-(PRO-PRO-GLY)4
E: COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY)4-HYP-HYP-GLY-(PRO-PRO-GLY)4
F: COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY)4-HYP-HYP-GLY-(PRO-PRO-GLY)4


Theoretical massNumber of molelcules
Total (without water)6,9353
Polymers6,9353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-26 kcal/mol
Surface area3890 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 MODEL PEPTIDES (PRO-PRO-GLY)4-HYP-HYP-GLY-(PRO-PRO-GLY)4


Mass: 2311.547 Da / Num. of mol.: 6 / Source method: obtained synthetically
Details: THIS COLLAGEN MODEL TRIPLETT WAS CHEMICALLY SYSTHESIZED. Hyp-Hyp-Gly guest in Pro-Pro-Gly host peptide.
References: UniProt: Q80BK4*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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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: 1.83 Å3/Da / Density % sol: 32.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 1000, ACETATE BUFFER, pH 5.6, 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 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 30, 2004 / Details: 1.1-M-LONG BENT-PLANE MIRROR
RadiationMonochromator: Trianglualr Si(111) with an asymmetric angle of 7.8
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.22→26.61 Å / Num. obs: 32577 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Redundancy: 3.52 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 4.5
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
CrystalCleardata collection
CrystalCleardata reduction
X-PLORmodel building
SHELXL-97refinement
HKL-2000data reduction
CrystalCleardata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 2CUO

2cuo


Resolution: 1.22→8 Å / Num. parameters: 10425 / Num. restraintsaints: 12967 / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: THE POLYMER STRUCTURE CAN BE GENERATED FROM THE SUBMITTED ASYMMETRIC UNIT BY APPLYING THE (0 0 1) TRANSLATION USING FRACTIONAL COORDINATES. BOTH UP- AND DOWN- PUCKERINGS WERE OBSERVED FOR ...Details: THE POLYMER STRUCTURE CAN BE GENERATED FROM THE SUBMITTED ASYMMETRIC UNIT BY APPLYING THE (0 0 1) TRANSLATION USING FRACTIONAL COORDINATES. BOTH UP- AND DOWN- PUCKERINGS WERE OBSERVED FOR PROLINE RING AT THE X POSITION OF THE GLY-X-Y SEQUENCE. ANISOTROPIC REFINEMENT REDUCED FREE R.
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 1627 5.1 %RANDOM
Rwork0.1934 ---
all0.1964 32044 --
obs0.1964 32044 --
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 823 / Occupancy sum non hydrogen: 1158
Refinement stepCycle: LAST / Resolution: 1.22→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms895 0 0 263 1158
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0282
X-RAY DIFFRACTIONs_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.047
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.145
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0.076

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