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- PDB-1a3j: X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A COLLAGEN-LIKE PEPTIDE W... -

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Basic information

Entry
Database: PDB / ID: 1a3j
TitleX-RAY CRYSTALLOGRAPHIC DETERMINATION OF A COLLAGEN-LIKE PEPTIDE WITH THE REPEATING SEQUENCE (PRO-PRO-GLY)
Components(COLLAGEN-LIKE PEPTIDE) x 2
KeywordsEXTRACELLULAR MATRIX / COLLAGEN
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsKramer, R.Z. / Vitagliano, L. / Bella, J. / Berisio, R. / Mazzarella, L. / Brodsky, B. / Zagari, A. / Berman, H.M.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: X-ray crystallographic determination of a collagen-like peptide with the repeating sequence (Pro-Pro-Gly).
Authors: Kramer, R.Z. / Vitagliano, L. / Bella, J. / Berisio, R. / Mazzarella, L. / Brodsky, B. / Zagari, A. / Berman, H.M.
History
DepositionJan 22, 1998Processing site: BNL
Revision 1.0May 6, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

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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)1,8133
Polymers1,8133
Non-polymers00
Water72140
1
A: COLLAGEN-LIKE PEPTIDE
B: COLLAGEN-LIKE PEPTIDE
C: COLLAGEN-LIKE PEPTIDE
x 5


Theoretical massNumber of molelcules
Total (without water)9,06515
Polymers9,06515
Non-polymers00
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation1_557x,y,z+21
crystal symmetry operation1_558x,y,z+31
crystal symmetry operation1_559x,y,z+41
Unit cell
Length a, b, c (Å)27.010, 26.420, 20.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE 21 RESIDUE ASYMMETRIC UNIT CORRESPONDS TO ONE TRIPLE-HELICAL REPEAT AND IS SMALLER THAN THE ENTIRE 90 RESIDUE PEPTIDE DUE TO TRANSLATIONAL DISORDER ALONG THE HELICAL AXIS. THE RESULT IS A POLYMER-LIKE STRUCTURE WITH NO DEFINED ENDS. THE POLYMER STRUCTURE IS FORMED BY CONTINUATION OF THE CHAINS USING THE SYMMETRY-RELATED MOLECULES ALONG THE HELICAL AXIS. THE TVECT RECORD BELOW PRESENTS THE TRANSLATION THAT WILL GENERATE THE POLYMER. NOTE: THEREFORE, CLOSE CONTACTS BETWEEN SYMMETRY-RELATED MOLECULES ARE INTENTIONAL AND NECESSARY. INTERCHAIN HYDROGEN BONDING AT THE END OF CHAINS ALSO UTILIZES SYMMETRY-RELATED MOLECULES. THE 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 1 - 9 BY (0 0 1), (0 0 2), AND (0 0 3) AND RESIDUES 7 - 9 BY (0 0 4). CHAIN B: TRANSLATE RESIDUES 31 - 36 BY (0 0 1), (0 0 2), AND (0 0 3). CHAIN C: TRANSLATE RESIDUES 61 - 66 BY (0 0 1), (0 0 2), AND (0 0 3) AND RESIDUES 64 - 66 BY (004). 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: 771.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#2: Protein/peptide COLLAGEN-LIKE PEPTIDE


Mass: 520.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHYDROGEN BONDS BETWEEN PEPTIDE CHAINS FOLLOW THE RICH AND CRICK MODEL II FOR COLLAGEN.
Sequence detailsFOR EACH CHAIN, RESIDUE NUMBERING CORRESPONDS TO THE ENTIRE MOLECULE RATHER THAN THE SHORTER ASYMMETRIC UNIT.

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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: 1.99 Å3/Da / Density % sol: 38.31 %
Crystal growDetails: PEPTIDE WAS CRYSTALIZED FROM 7.5 MG/ML PEPTIDE (DISSOLVED IN 5% V/V AQUEOUS ACETIC ACID) AND 0.05 M SODIUM ACETATE.
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlpeptide1drop
25 %(v/v)acetic acid1drop
30.05 Msodium acetate1drop
40.1 Macetate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.91
DetectorType: PRINCETON 2K / Detector: CCD / Date: Oct 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionHighest resolution: 1.6 Å / Num. obs: 1836 / % possible obs: 86 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.049
Reflection shellResolution: 1.6→1.8 Å / % possible all: 60
Reflection shell
*PLUS
% possible obs: 60 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
HKL(SCALEPACK)data scaling
X-PLOR3.1phasing
RefinementResolution: 1.6→8 Å / Isotropic thermal model: RESTRAINED / σ(F): 2
Details: DUE TO THE QUASI-INFINITE NATURE OF THE TRIPLE HELIX, DURING REFINEMENT COVALENT BONDS ARE NECESSARY TO JOIN THE MOLECULE WITH ITS SYMMETRY MATES BOTH ABOVE IT AND BELOW IT ALONG THE HELICAL ...Details: DUE TO THE QUASI-INFINITE NATURE OF THE TRIPLE HELIX, DURING REFINEMENT COVALENT BONDS ARE NECESSARY TO JOIN THE MOLECULE WITH ITS SYMMETRY MATES BOTH ABOVE IT AND BELOW IT ALONG THE HELICAL AXIS AND TIGHT REFINEMENT CONSTRAINTS WERE MAINTAINED. THE UNIT CELL AXES WERE CHOSEN TO COINCIDE WITH A PREVIOUS STRUCTURE DETERMINATION (OKUYAMA 1981) OF THIS PEPTIDE.
RfactorNum. reflection
Rwork0.213 -
obs0.213 1736
Displacement parametersBiso mean: 21.1 Å2
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms126 0 0 40 166
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.99
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.99

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