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- PDB-1v7h: Crystal Structures of Collagen Model Peptides with Pro-Hyp-Gly Se... -

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Basic information

Entry
Database: PDB / ID: 1v7h
TitleCrystal Structures of Collagen Model Peptides with Pro-Hyp-Gly Sequence at 1.26 A
Components(Collagen like peptide) x 3
KeywordsSTRUCTURAL PROTEIN / Collagen / Triple-helix / Model peptide
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsOkuyama, K. / Hongo, C. / Fukushima, R. / Wu, G. / Narita, H. / Noguchi, K. / Tanaka, Y. / Nishino, N.
CitationJournal: Biopolymers / Year: 2004
Title: Crystal structures of collagen model peptides with Pro-Hyp-Gly repeating sequence at 1.26 A resolution: implications for proline ring puckering
Authors: Okuyama, K. / Hongo, C. / Fukushima, R. / Wu, G. / Narita, H. / Noguchi, K. / Tanaka, Y. / Nishino, N.
History
DepositionDec 17, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 25, 2013Group: Derived calculations
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagen like peptide
B: Collagen like peptide
C: Collagen like peptide


Theoretical massNumber of molelcules
Total (without water)1,9253
Polymers1,9253
Non-polymers00
Water88349
1
A: Collagen like peptide
B: Collagen like peptide
C: Collagen like peptide

A: Collagen like peptide
B: Collagen like peptide
C: Collagen like peptide


Theoretical massNumber of molelcules
Total (without water)3,8506
Polymers3,8506
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Unit cell
Length a, b, c (Å)13.892, 26.115, 19.954
Angle α, β, γ (deg.)90.00, 105.95, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE ENTIRE 30 RESIDUE LONG PEPTIDE CAN BE GENERATED FROM THE SUBMITTED ASYMMETRIC UNIT BY APPLYING THE FOLLOWING TRANSLATIONS (USING FRACTIONAL COORDINATES): CHAIN A: TRANSLATE RESIDUES 2 - 7 BY (001), AND RESIDUES 1-7 BY (002),(003),(004), AND RESIDUES 1-4 BY (005) CHAIN B: TRANSLATE RESIDUES 3 - 7 BY (001), AND RESIDUES 1-7 BY (002),(003),(004) AND RESIDUE 1-2 BY (005). CHAIN C: TRANSLATE RESIDUES 1 - 7 BY (001),(002),(003),(004), AND RESIDUES 1-3 BY (005). THIS WILL RESULT IN A MOLECULE WITH A TOTAL OF 90 RESIDUES, 30 IN EACH CHAIN.

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Components

#1: Protein/peptide Collagen like peptide


Mass: 609.630 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Pro-Hyp-Gly triplet is very popular in collagen sequence
#2: Protein/peptide Collagen like peptide


Mass: 665.693 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Pro-Hyp-Gly triplet is very popular in collagen sequence
#3: Protein/peptide Collagen like peptide


Mass: 649.693 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Pro-Hyp-Gly triplet is very popular in collagen sequence
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 1.81 Å3/Da / Density % sol: 31.96 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop
Details: PEG200, ACETIC ACID, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: OXFORD PX210 / Detector: CCD / Date: Jun 11, 2002 / Details: MIRROR-MONOCHROMATOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.24→20 Å / Num. obs: 3257 / Observed criterion σ(F): 1 / Rmerge(I) obs: 0.042
Reflection shellResolution: 1.24→1.28 Å / Rmerge(I) obs: 0.057 / Mean I/σ(I) obs: 8.2 / Num. unique all: 290 / % possible all: 74

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
CrystalCleardata reduction
CrystalClear(MSC/RIGAKU)data scaling
SHELXSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: (PRO-HYP-GLY)10 structure reported in V.NAGARAJAN, S.KAMITORI, K.OKUYAMA, J.BIOCHEM.,125, 310 (1999).

Resolution: 1.25→10 Å / Num. parameters: 1396 / Num. restraintsaints: 1695 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1828 158 4.7 %RANDOM
Rwork0.1271 ---
all-3176 --
obs-3173 78.2 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 112 / Occupancy sum non hydrogen: 182
Refinement stepCycle: LAST / Resolution: 1.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms133 0 0 49 182
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0368
X-RAY DIFFRACTIONs_zero_chiral_vol0.106
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.029
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.031
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.25→1.3 Å /
RfactorNum. reflection
Rwork0.126 -
obs-315

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