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- PDB-1v4f: Crystal structures of collagen model peptides with pro-hyp-gly se... -

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Basic information

Entry
Database: PDB / ID: 1v4f
TitleCrystal structures of collagen model peptides with pro-hyp-gly sequence at 1.3A
Components(collagen like peptide) x 3
KeywordsSTRUCTURAL PROTEIN / Collagen / triple-helix
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsOkuyama, K. / Hongo, C. / Fukushima, R. / Wu, G. / 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
DepositionNov 13, 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

Downloads & links

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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


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)13.864, 26.181, 19.877
Angle α, β, γ (deg.)90.00, 105.75, 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 2 - 7 BY (001), AND RESIDUES 1-7 BY (002), (003), (004), (005). CHAIN B: TRANSLATE RESIDUES 3 - 7 BY (001), AND RESIDUES 1-7 BY (002), (003), (004) AND RESIDUE 1-5 BY (005). CHAIN C: TRANSLATE RESIDUES 1 - 7 BY (001), (002), (003) (004), AND RESIDUES 1-6 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: This triplet is very popular in the collagen sequence.
#2: Protein/peptide collagen like peptide


Mass: 665.693 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This triplet is very popular in the collagen sequence.
#3: Protein/peptide collagen like peptide


Mass: 649.693 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This triplet is very popular in the 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: 1.8 Å3/Da / Density % sol: 31.8 %
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 / 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: 1.26→20 Å / Num. all: 3592 / Num. obs: 3520 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 6.67 % / Rmerge(I) obs: 0.06 / Rsym value: 0.035 / Net I/σ(I): 3.3
Reflection shellResolution: 1.26→1.32 Å / Redundancy: 4.66 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.3 / Num. unique all: 419 / % possible all: 79

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Processing

Software
NameClassification
CrystalCleardata collection
CrystalCleardata reduction
SHELXmodel building
SHELXL-97refinement
CrystalCleardata scaling
X-PLORphasing
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: 1.26→10 Å / Num. parameters: 1396 / 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. Both up- and down- puckerings were observed for ...Details: The polymer structure can be generated from the submitted asymmetric unit by applying the (0 0 1) translation using fractional coordinates. Both up- and down- puckerings were observed for proline ring at the X position of the Gly-X-Y sequence.
RfactorNum. reflection% reflectionSelection details
Rfree0.159 176 5 %RANDOM
Rwork0.1332 ---
all-3520 --
obs-3344 95 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 112 / Occupancy sum non hydrogen: 182
Refinement stepCycle: LAST / Resolution: 1.26→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms133 0 0 49 182
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.055
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0336
X-RAY DIFFRACTIONs_zero_chiral_vol0.08
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.011
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.035
X-RAY DIFFRACTIONs_approx_iso_adps0

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