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- PDB-1a3i: X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A COLLAGEN-LIKE PEPTIDE W... -

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Basic information

Entry
Database: PDB / ID: 1a3i
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
Function / homologyACETIC ACID
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 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 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Apr 3, 2024Group: 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,9335
Polymers1,8133
Non-polymers1202
Water66737
1
A: COLLAGEN-LIKE PEPTIDE
B: COLLAGEN-LIKE PEPTIDE
C: COLLAGEN-LIKE PEPTIDE
hetero molecules
x 5


Theoretical massNumber of molelcules
Total (without water)9,66625
Polymers9,06515
Non-polymers60110
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)26.820, 26.290, 20.180
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: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 1.95 Å3/Da / Density % sol: 36.82 %
Crystal growDetails: PEPTIDE WAS CRYSTALLIZED FROM 4.0 MG/ML PEPTIDE IN 10% ACETIC ACID, 0.1% SODIUM AZIDE, AND 3.0% PEG400.
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14.0 mg/mlpeptide1drop
210 %(v/v)acetic acid1drop
30.1 %(w/v)sodium azide1drop
43.0 %(w/v)PEG4001drop
56.0 %(w/v)PEG4001reservoir

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Data collection

DiffractionMean temperature: 259 K
Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Oct 1, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.97 Å / Num. obs: 1136 / % possible obs: 99.5 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.97→2.2 Å / % possible all: 98
Reflection
*PLUS
% possible obs: 100 %
Reflection shell
*PLUS
Rmerge(I) obs: 98

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
LALSrefinement
MOLENdata reduction
X-PLOR3.1phasing
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IDEALIZED SEVEN-FOLD TRIPLE-HELIX

Resolution: 1.97→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: GROUP / σ(F): 2
Details: DUE TO THE QUASI-INFINITE, AVERAGED 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 ...Details: DUE TO THE QUASI-INFINITE, AVERAGED 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% reflection
Rwork0.181 --
obs0.181 861 76.7 %
Displacement parametersBiso mean: 15.9 Å2
Refinement stepCycle: LAST / Resolution: 1.97→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms126 0 0 45 171
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg2.07
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_d2.11
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
LS refinement shellResolution: 1.97→2.04 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.22 69 -
obs--63.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
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_deg2.11

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