+Open data
-Basic information
Entry | Database: PDB / ID: 3a0m | ||||||
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Title | Structure of (PPG)4-OVG-(PPG)4, monoclinic, twinned crystal | ||||||
Components | collagen-like peptide | ||||||
Keywords | STRUCTURAL PROTEIN / collagen / triple-helix / model peptide / twinned crystal | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å | ||||||
Authors | Okuyama, K. / Morimoto, T. / Mizuno, K. / Bachinger, H.P. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a0m.cif.gz | 66.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a0m.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 3a0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/3a0m ftp://data.pdbj.org/pub/pdb/validation_reports/a0/3a0m | HTTPS FTP |
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-Related structure data
Related structure data | 3a1hC 3admC 2cuoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 2297.563 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: THIS PEPTIDE WAS CHEMICALLY SYSTHESIZED. #2: Water | ChemComp-HOH / | Sequence details | THIS 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 MICROHETER | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 38.41 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.7 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Mar 13, 2007 Details: double-crystal monochromator & horizontal focusing mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.395 |
Reflection | Resolution: 0.98→24.8 Å / Num. obs: 60025 / % possible obs: 97 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.05 |
Reflection shell | Resolution: 0.98→1.02 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.35 / Num. unique all: 6010 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 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.
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Refine analyze | Num. disordered residues: 10 / Occupancy sum hydrogen: 847 / Occupancy sum non hydrogen: 1173.61 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.02→24.8 Å
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Refine LS restraints |
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LS refinement shell |
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