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- PDB-9cqi: CRYSTAL STRUCTURE OF GAGA-DOG HSP47(36-418) IN COMPLEX WITH ADNEC... -

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Basic information

Entry
Database: PDB / ID: 9cqi
TitleCRYSTAL STRUCTURE OF GAGA-DOG HSP47(36-418) IN COMPLEX WITH ADNECTIN-44
Components
  • Serpin H1
  • anti-HSP47 Adnectin-44
KeywordsCHAPERONE / SERPIN H1
Function / homology
Function and homology information


collagen trimer / collagen fibril organization / collagen binding / serine-type endopeptidase inhibitor activity / endoplasmic reticulum / extracellular space
Similarity search - Function
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
Biological speciesCanis lupus familiaris (dog)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.941 Å
AuthorsSheriff, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2024
Title: Improving the diffraction quality of heat-shock protein 47 crystals.
Authors: Kish, K. / Cobell, S. / Szapiel, N. / Yan, C. / Newitt, J.A. / Tredup, J. / Rodrigo, I. / Tomasco, E. / Gao, M. / Marsilio, F. / Haugner, J. / Lipovsek, D. / Deng, B. / Bousquet, P. / Zhang, ...Authors: Kish, K. / Cobell, S. / Szapiel, N. / Yan, C. / Newitt, J.A. / Tredup, J. / Rodrigo, I. / Tomasco, E. / Gao, M. / Marsilio, F. / Haugner, J. / Lipovsek, D. / Deng, B. / Bousquet, P. / Zhang, Y. / Schmidt, H. / Sheriff, S.
History
DepositionJul 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serpin H1
B: anti-HSP47 Adnectin-44


Theoretical massNumber of molelcules
Total (without water)55,3472
Polymers55,3472
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-15 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.329, 82.521, 98.324
Angle α, β, γ (deg.)90, 116.14, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Serpin H1 / HSP47 / Collagen-binding protein


Mass: 43337.605 Da / Num. of mol.: 1 / Fragment: residues 36-418
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: SERPINH1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C7C419
#2: Protein anti-HSP47 Adnectin-44


Mass: 12009.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Derived from human fibronectin type III tenth domain (residues 1416-1509 of 1FNF), but not only are the residues in the BC, DE, FG loops varied, the lengths of the loops are also varied.
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.1 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4 M Sodium Malonate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.941→88.268 Å / Num. obs: 36513 / % possible obs: 93.6 % / Redundancy: 3.51 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.997 / CC1/2 anomalous: -0.072 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.0589 / Rrim(I) all: 0.1112 / AbsDiff over sigma anomalous: 0.769 / Baniso tensor eigenvalue 1: 0 Å2 / Baniso tensor eigenvalue 2: 7.122 Å2 / Baniso tensor eigenvalue 3: 17.9535 Å2 / Baniso tensor eigenvector 1 ortho1: 0.9628 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: -0.2702 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0.2702 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 0.9628 / Aniso diffraction limit 1: 1.877 Å / Aniso diffraction limit 2: 2.082 Å / Aniso diffraction limit 3: 2.409 Å / Aniso diffraction limit axis 1 ortho1: 0.97905 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: -0.20349 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0.20349 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 0.97905 / Net I/σ(I): 9.69 / Num. measured all: 127998 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 89.8 / % possible ellipsoidal: 93.6 / % possible ellipsoidal anomalous: 89.8 / % possible spherical: 72.9 / % possible spherical anomalous: 69.8 / Redundancy anomalous: 1.81 / Signal type: local
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
5.915-88.2683.650.028930.5966536653182518250.999-0.2340.01760.03390.68299.599.399.599.399.51.9199.3
4.679-5.9153.40.035426.2362006200182618260.9980.0090.02270.04220.77797.699.597.699.597.61.7699.5
4.077-4.6793.130.035425.4957165716182518250.998-0.1680.02380.04280.79789.299.289.299.289.21.6699.2
3.699-4.0773.420.044721.8862406240182718270.997-0.1050.02830.0530.78692.999.492.999.492.91.7999.4
3.433-3.6993.520.056618.6564256425182418240.996-0.1140.03530.06680.79595.699.495.699.495.61.8299.4
3.229-3.4333.580.071814.9365326532182618260.995-0.080.04440.08460.80296.999.696.999.696.91.8499.6
3.065-3.2293.630.099811.4466226622182618260.991-0.0710.06120.11730.78997.999.997.999.997.91.8699.9
2.932-3.0653.660.14078.3866926692182618260.981-0.030.08580.1650.78898.499.998.499.998.41.8899.9
2.817-2.9323.670.18746.4866966696182618260.97-0.0510.11420.21990.77998.299.998.299.998.21.8899.9
2.719-2.8173.70.23725.2267516751182618260.954-0.040.14310.27740.76498.599.698.599.698.51.8999.6
2.634-2.7193.440.29174.0362666266182318230.917-0.0190.18560.34660.76497.199.797.199.797.11.7699.7
2.558-2.6343.360.39763.0161406140182718270.862-0.0020.25720.47480.75197.899.897.899.897.81.7299.8
2.49-2.5583.50.39833.0163886388182518250.871-0.0570.24940.4710.74596.399.296.399.296.31.899.2
2.425-2.493.170.47192.4257965796182618260.781-0.0890.31580.56970.7528393.88393.8831.6693.8
2.363-2.4253.350.47622.4461186118182718270.812-0.0420.30620.56760.74980.790.180.78879.21.7490.1
2.302-2.3633.470.54742.2263266326182518250.742-0.140.34340.64770.74484.490.984.480.775.31.890.9
2.237-2.3023.540.60362.0764676467182518250.743-0.0180.37430.71180.76682.286.782.269.265.91.8386.7
2.172-2.2373.620.61462.0466166616182718270.7140.0380.37580.72160.77582.184.482.159.858.51.8684.4
2.097-2.1723.660.67121.8566846684182418240.6770.0160.40840.78680.76477.779.977.746.545.41.8779.9
1.941-2.0973.650.84721.5266706670182718270.5470.0470.51630.99350.81265.866.965.817.717.31.8766.9

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Processing

Software
NameVersionClassification
autoPROCdata processing
XDSJan 10, 2022data reduction
Aimless0.7.8data scaling
STARANISO2.3.87data scaling
BUSTER2.11.8refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.941→26.71 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.382 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.198 / SU Rfree Blow DPI: 0.17 / SU Rfree Cruickshank DPI: 0.174
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 1833 -RANDOM
Rwork0.2138 ---
obs0.2153 36497 72.9 %-
Displacement parametersBiso mean: 34.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.022 Å2
2---0.4833 Å20 Å2
3---0.4132 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.941→26.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 0 170 3965
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087610HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0213764HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2225SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1214HARMONIC5
X-RAY DIFFRACTIONt_it3895HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion508SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact6196SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.44
X-RAY DIFFRACTIONt_other_torsion16.77
LS refinement shellResolution: 1.941→2.04 Å
RfactorNum. reflection% reflection
Rfree0.3037 38 -
Rwork0.2752 --
obs--10.63 %

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