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- PDB-3a0m: Structure of (PPG)4-OVG-(PPG)4, monoclinic, twinned crystal -

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Basic information

Entry
Database: PDB / ID: 3a0m
TitleStructure of (PPG)4-OVG-(PPG)4, monoclinic, twinned crystal
Componentscollagen-like peptide
KeywordsSTRUCTURAL PROTEIN / collagen / triple-helix / model peptide / twinned crystal
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
AuthorsOkuyama, K. / Morimoto, T. / 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
DepositionMar 21, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references / Other
Revision 1.3Jun 6, 2012Group: Database references
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_poly_seq_scheme / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_poly_seq_scheme.auth_seq_num / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)13,7856
Polymers13,7856
Non-polymers00
Water5,044280
1
A: collagen-like peptide
B: collagen-like peptide
C: collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)6,8933
Polymers6,8933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-28 kcal/mol
Surface area3990 Å2
MethodPISA
2
D: collagen-like peptide
E: collagen-like peptide
F: collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)6,8933
Polymers6,8933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-29 kcal/mol
Surface area3920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.124, 26.366, 79.939
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
collagen-like peptide


Mass: 2297.563 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.: 280 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE ADOPTS A TRIPLE-HELICAL STRUCTURE SIMILAR TO THE COLLAGEN-HELIX. THE RESIDUES PRO F ...THIS SEQUENCE ADOPTS A TRIPLE-HELICAL STRUCTURE SIMILAR TO THE COLLAGEN-HELIX. THE RESIDUES PRO F 13, PRO F 14, HYP F 16, VAL F 17 ASSIGNED ALTERNATE POSITION B ARE MICROHETEROGENEITY.

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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: 1.86 Å3/Da / Density % sol: 38.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 11.3%(W/V) PEG 2000, 0.05M ACETATE BUFFER, PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.7 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Mar 13, 2007
Details: double-crystal monochromator & horizontal focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.395
ReflectionResolution: 0.98→24.8 Å / Num. obs: 60025 / % possible obs: 97 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.05
Reflection shellResolution: 0.98→1.02 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.35 / Num. unique all: 6010 / % possible all: 98.1

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2CUO

2cuo


Resolution: 1.02→24.8 Å / Num. parameters: 10851 / Num. restraintsaints: 13920 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: THE STRUCTURE WAS REFINED UNDER THE TWINNING OPERATOR (H,-K,-L) AND THE TWINNING FRACTION 0.395 USING THE TWINNED DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.1429 2698 -RANDOM
Rwork0.1161 ---
obs-51506 92.1 %-
Refine analyzeNum. disordered residues: 10 / Occupancy sum hydrogen: 847 / Occupancy sum non hydrogen: 1173.61
Refinement stepCycle: LAST / Resolution: 1.02→24.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms925 0 0 280 1205
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0321
X-RAY DIFFRACTIONs_zero_chiral_vol0.087
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.064
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.017
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.043
X-RAY DIFFRACTIONs_approx_iso_adps0.087
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.02-1.060.178X-RAY DIFFRACTION52876
1.06-1.10.156X-RAY DIFFRACTION51356
1.1-1.150.13X-RAY DIFFRACTION52046
1.15-1.210.114X-RAY DIFFRACTION51606
1.21-1.290.111X-RAY DIFFRACTION50746
1.29-1.380.103X-RAY DIFFRACTION51626

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