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- PDB-4axy: A molecular basis for the action of the collagen-specific chapero... -

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Basic information

Entry
Database: PDB / ID: 4axy
TitleA molecular basis for the action of the collagen-specific chaperone Hsp47-SERPINH1 and its structure-specific client recognition.
ComponentsCOLLAGEN-LIKE PEPTIDE
KeywordsSTRUCTURAL PROTEIN / CMP
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsWidmer, C. / Gebauer, J.M. / Brunstein, E. / Rosenbaum, S. / Zaucke, F. / Droegmueller, C. / Leeb, T. / Baumann, U.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Molecular Basis for the Action of the Collagen-Specific Chaperone Hsp47/Serpinh1 and its Structure-Specific Client Recognition.
Authors: Widmer, C. / Gebauer, J.M. / Brunstein, E. / Rosenbaum, S. / Zaucke, F. / Drogemuller, C. / Leeb, T. / Baumann, U.
History
DepositionJun 15, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Oct 28, 2015Group: Refinement description / Source and taxonomy

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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)4,8413
Polymers4,8413
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-23.4 kcal/mol
Surface area3280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.670, 45.670, 34.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2008-

HOH

21A-2013-

HOH

31B-2008-

HOH

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Components

#1: Protein/peptide COLLAGEN-LIKE PEPTIDE / HSP47 BINDING COLLAGEN-LIKE PEPTIDE


Mass: 1613.817 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsACETYL GROUP (ACE): THE N-TERMINUS WAS ACETYLATED TO PREVENT CHARGES. AMINO GROUP (NH2): THE C- ...ACETYL GROUP (ACE): THE N-TERMINUS WAS ACETYLATED TO PREVENT CHARGES. AMINO GROUP (NH2): THE C-TERMINUS WAS AM AMIDATED TO PREVENT CHARGES.

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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: 1.48 Å3/Da / Density % sol: 16.7 %
Description: MR WAS DONE WITH PARTS OF THE STRUCTURE PUBLISHED IN THE SAME ARTICLE AS THIS ENTRY.
Crystal growpH: 5.75
Details: 3.15 M AMMONIUM SULFATE, 0.05 M CITRIC ACID PH 5.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.24→100 Å / Num. obs: 10802 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 12.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.6
Reflection shellResolution: 1.24→1.31 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_1051)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→32.294 Å / SU ML: 0.12 / σ(F): 1.18 / Phase error: 20.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1728 539 5 %
Rwork0.1499 --
obs0.1511 10764 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.24→32.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms348 0 0 68 416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011396
X-RAY DIFFRACTIONf_angle_d1.444549
X-RAY DIFFRACTIONf_dihedral_angle_d7.786176
X-RAY DIFFRACTIONf_chiral_restr0.03941
X-RAY DIFFRACTIONf_plane_restr0.00889
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.36480.21111300.17242479X-RAY DIFFRACTION100
1.3648-1.56230.18711330.14352517X-RAY DIFFRACTION100
1.5623-1.96830.15011340.13362547X-RAY DIFFRACTION100
1.9683-32.30450.17341420.15392682X-RAY DIFFRACTION100

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