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- PDB-3ah9: Crystal structure of (Pro-Pro-Gly)9 at 1.1 A resolution -

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Basic information

Entry
Database: PDB / ID: 3ah9
TitleCrystal structure of (Pro-Pro-Gly)9 at 1.1 A resolution
Componentscollagen-like peptide
KeywordsSTRUCTURAL PROTEIN / collagen / triple helix / model peptide
Function / homology
Function and homology information


extracellular matrix structural constituent conferring tensile strength / extracellular matrix organization / extracellular space / membrane
Similarity search - Function
Saimiri transformation-associated protein / Collagen triple helix repeat / Collagen triple helix repeat (20 copies)
Similarity search - Domain/homology
ACETIC ACID / AZIDE ION / Saimiri transformation-associated protein
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsOkuyama, K. / Morimoto, T. / Hongo, C. / Hosaka, N. / Nishino, N.
CitationJournal: To be Published
Title: Crystal structure of (Pro-Pro-Gly)9
Authors: Okuyama, K. / Morimoto, T. / Hongo, C. / Hosaka, N. / Nishino, N.
History
DepositionApr 22, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 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_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,96512
Polymers13,6776
Non-polymers2886
Water4,630257
1
A: collagen-like peptide
B: collagen-like peptide
C: collagen-like peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9235
Polymers6,8393
Non-polymers842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-25 kcal/mol
Surface area4080 Å2
MethodPISA
2
D: collagen-like peptide
E: collagen-like peptide
F: collagen-like peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0437
Polymers6,8393
Non-polymers2044
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-25 kcal/mol
Surface area3790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.416, 25.990, 80.241
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. / References: UniProt: Q80BK4*PLUS
#2: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: N3
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 1.86 Å3/Da / Density % sol: 38.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 11.3% PEG 200, 5%(v/v) acetic acid, 0.5%(w/v) sodium azide, 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 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 25, 2004 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l
ReflectionResolution: 1.08→10 Å / Num. obs: 46590 / % possible obs: 98.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 7.1
Reflection shellResolution: 1.08→1.12 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.254 / Num. unique all: 4626 / % possible all: 100

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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: 1.08→10 Å / Num. parameters: 10345 / Num. restraintsaints: 12873 / 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) using the twinned data.
RfactorNum. reflection% reflectionSelection details
Rfree0.1906 2325 -RANDOM
Rwork0.1645 ---
obs-46579 93.9 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1149
Refinement stepCycle: LAST / Resolution: 1.08→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms872 0 20 257 1149
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0336
X-RAY DIFFRACTIONs_zero_chiral_vol0.077
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.066
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.017
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.061
X-RAY DIFFRACTIONs_approx_iso_adps0.104
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.08-1.120.24X-RAY DIFFRACTION46956
1.12-1.170.2X-RAY DIFFRACTION43516
1.17-1.220.193X-RAY DIFFRACTION42896
1.22-1.280.187X-RAY DIFFRACTION45406
1.28-1.360.178X-RAY DIFFRACTION42646
1.36-1.460.16X-RAY DIFFRACTION44226

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