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- PDB-3ai6: Triple-helical structure of (D-Pro-D-Pro-Gly)9 at 1.1 A resolution -

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Basic information

Entry
Database: PDB / ID: 3ai6
TitleTriple-helical structure of (D-Pro-D-Pro-Gly)9 at 1.1 A resolution
Componentscollagen-like peptide
KeywordsSTRUCTURAL PROTEIN / collagen helix / D-enantiomer
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: 1.1 Å
AuthorsOkuyama, K. / Miyama, K. / Kawaguchi, T. / Nishino, N.
CitationJournal: To be Published
Title: Triple-helical structure of (D-Pro-D-Pro-Gly)9
Authors: Okuyama, K. / Miyama, K. / Kawaguchi, T. / Nishino, N.
History
DepositionMay 10, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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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)13,6776
Polymers13,6776
Non-polymers00
Water4,504250
1
A: collagen-like peptide
B: collagen-like peptide
C: collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)6,8393
Polymers6,8393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: collagen-like peptide
E: collagen-like peptide
F: collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)6,8393
Polymers6,8393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.362, 25.920, 80.158
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-like peptide


Mass: 2279.547 Da / Num. of mol.: 6 / Source method: obtained synthetically
Details: This peptide adopts a collagen-helix with opposite chirality.
References: UniProt: Q80BK4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Sequence detailsTHE AUTHOR STATES, FOR THE SIX PEPTIDES, THE ACTUAL PEPTIDE CHAIN CONSISTS OF 27 AMINO ACID ...THE AUTHOR STATES, FOR THE SIX PEPTIDES, THE ACTUAL PEPTIDE CHAIN CONSISTS OF 27 AMINO ACID RESIDUES. THE B/F CHAIN CONSISTS OF TWO CHAINS WITH HALF OCCUPANCIES. THESE TWO CHAINS ARE ASSIGNED WITH ALTERNATE POSITION A AND B AND HAVE EXACTLY THE SAME ATOMIC COORDINATES PARTIALLY. DPR_4 DPR_5 GLY_6 (ALT. A) AND DPR_1 DPR_2 GLY_3 (ALT. B) ARE SAME. DPR_25 DPR_26 GLY_27 (ALT. A) AND DPR_22 DPR_23 GLY_24 (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: 1.62 Å3/Da / Density % sol: 38.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 11% PEG 200, 0.1M acetate buffer, pH 5.0, 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: RAYONIX MX225HE / Detector: CCD / Date: Dec 8, 2009
Details: A double-crystal monochromator and a horizontal focusing Mirror
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.484
ReflectionResolution: 1.04→50 Å / Num. obs: 50349 / % possible obs: 96.1 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 10.19
Reflection shellResolution: 1.04→1.06 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.72 / Num. unique all: 2337 / % possible all: 89.9

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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: 2CUO

2cuo


Resolution: 1.1→10 Å / Num. parameters: 11227 / Num. restraintsaints: 14206 / 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 TWINNING FRACTION 0.484 using the twinned data.
RfactorNum. reflection% reflectionSelection details
Rfree0.1829 2141 -RANDOM
Rwork0.1533 ---
all0.1533 ---
obs-42981 92 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1190.5
Refinement stepCycle: LAST / Resolution: 1.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms961 0 0 250 1211
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0316
X-RAY DIFFRACTIONs_zero_chiral_vol0.071
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.058
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.006
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.051
X-RAY DIFFRACTIONs_approx_iso_adps0.101
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.1-1.140.21X-RAY DIFFRACTION42066
1.14-1.190.183X-RAY DIFFRACTION39926
1.19-1.240.173X-RAY DIFFRACTION41056
1.24-1.310.168X-RAY DIFFRACTION41776
1.31-1.40.154X-RAY DIFFRACTION40566
1.4-1.510.141X-RAY DIFFRACTION40046

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