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- PDB-7bdu: Crystal structure of a Hsp47-collagen peptide complex -

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Basic information

Entry
Database: PDB / ID: 7bdu
TitleCrystal structure of a Hsp47-collagen peptide complex
Components
  • 21er collagen model peptide
  • Collagen-binding protein
KeywordsCHAPERONE / hsp / hsp47 / collagen
Function / homology
Function and homology information


Collagen biosynthesis and modifying enzymes / negative regulation of endopeptidase activity / collagen fibril organization / collagen binding / serine-type endopeptidase inhibitor activity / endoplasmic reticulum / extracellular space
Similarity search - Function
Serpin H1 / Serpin H1, serpin domain / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors
Similarity search - Domain/homology
Collagen-binding protein
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.49 Å
AuthorsAbraham, E.T. / Gebauer, J.M. / Baumann, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)73111208 Germany
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Collagen's primary structure determines collagen:HSP47 complex stoichiometry.
Authors: Abraham, E.T. / Oecal, S. / Morgelin, M. / Schmid, P.W.N. / Buchner, J. / Baumann, U. / Gebauer, J.M.
History
DepositionDec 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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-binding protein
B: Collagen-binding protein
C: 21er collagen model peptide
D: 21er collagen model peptide
E: 21er collagen model peptide
F: 21er collagen model peptide
G: 21er collagen model peptide
H: 21er collagen model peptide


Theoretical massNumber of molelcules
Total (without water)99,8428
Polymers99,8428
Non-polymers00
Water1,31573
1
A: Collagen-binding protein
C: 21er collagen model peptide
D: 21er collagen model peptide
E: 21er collagen model peptide


Theoretical massNumber of molelcules
Total (without water)49,9214
Polymers49,9214
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-35 kcal/mol
Surface area19080 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12790 Å2
ΔGint-68 kcal/mol
Surface area36200 Å2
MethodPISA
3
B: Collagen-binding protein
F: 21er collagen model peptide
G: 21er collagen model peptide
H: 21er collagen model peptide


Theoretical massNumber of molelcules
Total (without water)49,9214
Polymers49,9214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-34 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.821, 129.800, 173.372
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

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Components

#1: Protein Collagen-binding protein / Serpin H1


Mass: 44283.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: SERPINH1 / Production host: Escherichia coli (E. coli) / References: UniProt: E2RHY7
#2: Protein/peptide
21er collagen model peptide


Mass: 1879.144 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES, 18-26% PEG 3350, 1-6% Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→45.91 Å / Num. obs: 68330 / % possible obs: 99.02 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.125 / Net I/σ(I): 10.12
Reflection shellResolution: 2.49→2.59 Å / Rmerge(I) obs: 0.8 / Num. unique obs: 3406

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4au2

4au2


Resolution: 2.49→45.91 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.13 / Phase error: 29.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 3510 5.14 %
Rwork0.2175 64820 -
obs0.2201 68330 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.04 Å2 / Biso mean: 54.809 Å2 / Biso min: 28.39 Å2
Refinement stepCycle: final / Resolution: 2.49→45.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6653 0 0 73 6726
Biso mean---46.78 -
Num. residues----870
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.49-2.530.35941150.31862204231985
2.53-2.570.32581380.29652690282899
2.57-2.60.34471390.29882585272499
2.6-2.640.38622070.30442555276299
2.64-2.690.37191310.30322678280999
2.69-2.730.29691340.28952653278799
2.73-2.780.37261060.2962639274599
2.78-2.840.38031200.29362613273399
2.84-2.90.35841360.28612625276199
2.9-2.960.35361670.26952622278999
2.96-3.030.28341630.26192569273299
3.03-3.10.32261310.26322635276699
3.1-3.190.39571310.25552603273498
3.19-3.280.28071210.26192586270797
3.28-3.390.30481260.24712598272497
3.39-3.510.29961320.23512562269498
3.51-3.650.27961770.21332566274398
3.65-3.810.27531370.19692640277799
3.81-4.010.21321240.19142616274099
4.01-4.270.24141500.1812611276199
4.27-4.590.20671450.16422618276399
4.59-5.060.2221830.16212536271998
5.06-5.790.19471410.19172590273198
5.79-7.280.23771180.20762602272097
7.29-45.910.22591380.17242624276299

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