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- PDB-1x1k: Host-guest peptide (Pro-Pro-Gly)4-(Pro-alloHyp-Gly)-(Pro-Pro-Gly)4 -

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Basic information

Entry
Database: PDB / ID: 1x1k
TitleHost-guest peptide (Pro-Pro-Gly)4-(Pro-alloHyp-Gly)-(Pro-Pro-Gly)4
Components(Host-guest peptide (Pro-Pro-Gly)4-(Pro-alloHyp-Gly)-(Pro-Pro-Gly)4) x 2
KeywordsSTRUCTURAL PROTEIN / allo-Hyp / non-natural amino acid / collagen model peptide / puckering / triple-helix stability
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
AuthorsJiravanichanun, N. / Hongo, C. / Wu, G. / Noguchi, K. / Okuyama, K. / Nishino, N. / Silva, T.
Citation
Journal: Chembiochem / Year: 2005
Title: Unexpected puckering of hydroxyproline in the guest triplets, hyp-pro-gly and pro-allohyp-gly sandwiched between pro-pro-gly sequence
Authors: Jiravanichanun, N. / Hongo, C. / Wu, G. / Noguchi, K. / Okuyama, K. / Nishino, N. / Silva, T.
#1: Journal: To be Published
Title: High Resolution Structure of Collagen Model Peptide Sequence (Pro-Pro-Gly)4-(Pro-alloHyp-Gly)-(Pro-Pro-Gly)4
Authors: Jiravanichanun, N. / Noguchi, K. / Okuyama, K. / Nishino, N.
History
DepositionApr 5, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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

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Assembly

Deposited unit
A: Host-guest peptide (Pro-Pro-Gly)4-(Pro-alloHyp-Gly)-(Pro-Pro-Gly)4
B: Host-guest peptide (Pro-Pro-Gly)4-(Pro-alloHyp-Gly)-(Pro-Pro-Gly)4
C: Host-guest peptide (Pro-Pro-Gly)4-(Pro-alloHyp-Gly)-(Pro-Pro-Gly)4
D: Host-guest peptide (Pro-Pro-Gly)4-(Pro-alloHyp-Gly)-(Pro-Pro-Gly)4
E: Host-guest peptide (Pro-Pro-Gly)4-(Pro-alloHyp-Gly)-(Pro-Pro-Gly)4
F: Host-guest peptide (Pro-Pro-Gly)4-(Pro-alloHyp-Gly)-(Pro-Pro-Gly)4


Theoretical massNumber of molelcules
Total (without water)14,0416
Polymers14,0416
Non-polymers00
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10050 Å2
ΔGint-75 kcal/mol
Surface area7780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.445, 26.039, 80.309
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
Host-guest peptide (Pro-Pro-Gly)4-(Pro-alloHyp-Gly)-(Pro-Pro-Gly)4


Mass: 2295.547 Da / Num. of mol.: 5 / Source method: obtained synthetically / Details: collagen model peptide was chemically systhesized / References: UniProt: Q80BK4*PLUS
#2: Protein/peptide Host-guest peptide (Pro-Pro-Gly)4-(Pro-alloHyp-Gly)-(Pro-Pro-Gly)4


Mass: 2562.828 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: collagen model peptide was chemically systhesized / References: UniProt: Q80BK4*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 1.74 Å3/Da / Density % sol: 29.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG200, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.8, 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 21, 2004
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.81
211
ReflectionResolution: 1.1→30 Å / Num. all: 43582 / Num. obs: 43437 / % possible obs: 99.67 % / Observed criterion σ(F): 1
Reflection shellResolution: 1.1→1.14 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4376 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ITT

1itt


Resolution: 1.1→8 Å / Num. parameters: 11488 / Num. restraintsaints: 15246 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 2149 -RANDOM
Rwork0.1703 ---
all0.1731 41288 --
obs-43437 92.3 %-
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 855 / Occupancy sum non hydrogen: 1258
Refinement stepCycle: LAST / Resolution: 1.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 0 283 1275
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0386
X-RAY DIFFRACTIONs_zero_chiral_vol0.071
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.03
X-RAY DIFFRACTIONs_approx_iso_adps0.086

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