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- PDB-1v6q: Crystal Structures of Collagen Model Peptides with Pro-Hyp-Gly Se... -

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Basic information

Entry
Database: PDB / ID: 1v6q
TitleCrystal Structures of Collagen Model Peptides with Pro-Hyp-Gly Sequence at 1.3 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 3, 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
Water75742
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)14.051, 26.775, 20.004
Angle α, β, γ (deg.)90.00, 106.76, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE ENTIRE 33 RESIDUE LONG PEPTIDE CAN BE GENERATED FROM THE SUBMITTED ASYMMETRIC UNIT BY APPLYING THE FOLLOWING TRANSLATIONS (USING FRACTIONAL COORDINATES): CHAIN A: TRANSLATE RESIDUES 104-109 BY (001), AND RESIDUES 103-109 BY (002), (003), (004)(005). CHAIN B: TRANSLATE RESIDUES 204 - 208 BY (001), AND RESIDUES 202-208 BY (002), (003), (004) AND RESIDUE 202-206 BY (005). CHAIN C: TRANSLATE RESIDUES 301 - 307 BY (001), (002), (003) (004), AND RESIDUES 301-306 BY (005). THIS WILL RESULT IN A MOLECULE WITH A TOTAL OF 99 RESIDUES, 33 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.: 42 / 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: 1.87 Å3/Da / Density % sol: 34.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PEG 200, Acetic acid, Sodium azide, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2002 / Details: 1-M-LONG BENT-CYLINDER MIRROR
RadiationMonochromator: FIXED-EXIT DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→19.15 Å / Num. obs: 3768 / % possible obs: 94.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 7.6
Reflection shellResolution: 1.25→1.3 Å / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 2.4 / Num. unique all: 268 / % possible all: 67.7

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Processing

Software
NameClassification
CrystalCleardata collection
CrystalCleardata reduction
SHELXmodel building
SHELXL-97refinement
CrystalCleardata scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: (Pro-Hyp-Gly)10 structure reported in V.Nagarajan, S.Kamitori and K.Okuyama, J.Biochem., 125, 310 (1999).

Resolution: 1.25→10 Å / Num. parameters: 1368 / Num. restraintsaints: 1698 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
Details: The polymer structure can be generated from the submitted asymmetric unit by applying the (0 0 1) translation using fractional coordinates.
RfactorNum. reflection% reflectionSelection details
Rfree0.1886 186 5 %RANDOM
Rwork0.1346 ---
all-3733 --
obs-3547 89.1 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 112 / Occupancy sum non hydrogen: 175
Refinement stepCycle: LAST / Resolution: 1.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms133 0 0 42 175
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0314
X-RAY DIFFRACTIONs_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.033
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.014
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.037
X-RAY DIFFRACTIONs_approx_iso_adps0

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