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- PDB-3a19: Structure of (PPG)4-OOG-(PPG)4_H monoclinic, twinned crystal -

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Basic information

Entry
Database: PDB / ID: 3a19
TitleStructure of (PPG)4-OOG-(PPG)4_H monoclinic, twinned crystal
Componentscollagen-like peptide
KeywordsSTRUCTURAL PROTEIN / collagen / triple-helix / twinned crystal
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsOkuyama, K. / Morimoto, T. / Hyakutake, M. / Wu, G. / Mizuno, K. / Bachinger, H.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Two crystal modifications of (Pro-Pro-Gly)4-Hyp-Hyp-Gly-(Pro-Pro-Gly)4 reveal the puckering preference of Hyp(X) in the Hyp(X):Hyp(Y) and Hyp(X):Pro(Y) stacking pairs in collagen helices.
Authors: Okuyama, K. / Morimoto, T. / Narita, H. / Kawaguchi, T. / Mizuno, K. / Bachinger, H.P. / Wu, G. / Noguchi, K.
History
DepositionMar 28, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 17, 2014Group: Database references
Revision 1.3Nov 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

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)13,8696
Polymers13,8696
Non-polymers00
Water4,270237
1
A: collagen-like peptide
B: collagen-like peptide
C: collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)6,9353
Polymers6,9353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-26 kcal/mol
Surface area4120 Å2
MethodPISA
2
D: collagen-like peptide
E: collagen-like peptide
F: collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)6,9353
Polymers6,9353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-27 kcal/mol
Surface area4070 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9550 Å2
ΔGint-68 kcal/mol
Surface area7180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.649, 26.928, 79.656
Angle α, β, γ (deg.)90.00, 89.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
collagen-like peptide


Mass: 2311.547 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: THIS PEPTIDE WAS CHEMICALLY SYSTHESIZED.
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE ADOPTS A 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: 1.8 Å3/Da / Density % sol: 32.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 16.25%(w/v) PEG 1000, 0.05M acetate buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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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: Jun 25, 2004 / 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: 1.55→50 Å / Num. obs: 14850 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.081
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.35 / % possible all: 99.9

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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: 2CUO

2cuo


Resolution: 1.55→20 Å / Num. parameters: 4666 / Num. restraintsaints: 4206 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE STRUCTURE WAS REFINED UNDER THE TWINNING OPERATOR (H,-K,-L) AND THE TWINNING FRACTION 0.421 USING THE TWINNED DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 736 -RANDOM
Rwork0.1663 ---
obs-14833 94.2 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1165
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms928 0 0 237 1165
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0269
X-RAY DIFFRACTIONs_zero_chiral_vol0.052
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.052
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.005
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.067
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.54-1.610.219X-RAY DIFFRACTION14806
1.61-1.670.208X-RAY DIFFRACTION14096
1.67-1.750.186X-RAY DIFFRACTION13946
1.75-1.840.182X-RAY DIFFRACTION13836
1.84-1.950.159X-RAY DIFFRACTION13966
1.95-2.110.154X-RAY DIFFRACTION14266

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