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- PDB-9cqf: CRYSTAL STRUCTURE OF APO C-TERMINAL HIS-TAG DOG HSP47(36-418) IN ... -

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Basic information

Entry
Database: PDB / ID: 9cqf
TitleCRYSTAL STRUCTURE OF APO C-TERMINAL HIS-TAG DOG HSP47(36-418) IN A C 2 2 21 CRYSTAL FORM
ComponentsSerpin H1
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.928 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

Downloads & links

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Assembly

Deposited unit
A: Serpin H1
B: Serpin H1
D: Serpin H1
E: Serpin H1
F: Serpin H1
G: Serpin H1
H: Serpin H1
I: Serpin H1


Theoretical massNumber of molelcules
Total (without water)354,2698
Polymers354,2698
Non-polymers00
Water1267
1
A: Serpin H1


Theoretical massNumber of molelcules
Total (without water)44,2841
Polymers44,2841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serpin H1


Theoretical massNumber of molelcules
Total (without water)44,2841
Polymers44,2841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Serpin H1


Theoretical massNumber of molelcules
Total (without water)44,2841
Polymers44,2841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Serpin H1


Theoretical massNumber of molelcules
Total (without water)44,2841
Polymers44,2841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
F: Serpin H1


Theoretical massNumber of molelcules
Total (without water)44,2841
Polymers44,2841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
G: Serpin H1


Theoretical massNumber of molelcules
Total (without water)44,2841
Polymers44,2841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
H: Serpin H1


Theoretical massNumber of molelcules
Total (without water)44,2841
Polymers44,2841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
I: Serpin H1


Theoretical massNumber of molelcules
Total (without water)44,2841
Polymers44,2841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.78, 129.94, 501.93
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 44283.680 Da / Num. of mol.: 8 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 200 mM Lithium Citrate Tribasic, 20% (w/v) PEG 3350

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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 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.927→250.965 Å / Num. obs: 63276 / % possible obs: 93.9 % / Redundancy: 6.91 %
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 through the data processing procedure (rejection of overloaded or too partial reflections, outlier/misfit rejection 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: 0.992 / Rmerge(I) obs: 0.2196 / Rpim(I) all: 0.0894 / Rrim(I) all: 0.2374 / Net I/σ(I): 7.11 / Num. measured all: 437083
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
8.917-250.9656.750.06220.732136421364316431640.9970.02510.06799.9
7.035-8.9176.230.101114.281970019700316331630.9940.04350.1103100
6.121-7.0356.820.167910.232156221562316331630.9870.06890.181799.9
5.545-6.1217.060.19279.472233422334316531650.9830.07760.20899.8
5.138-5.5457.120.18929.752252522525316331630.9820.07610.204199.8
4.829-5.1387.170.18819.852270522705316531650.9840.07520.202899.9
4.583-4.8297.20.18439.992278822788316431640.9860.07360.198799.8
4.378-4.5836.550.19298.872072120721316231620.9810.08130.209799.9
4.207-4.3786.880.22498.192178221782316531650.9790.09230.243399.9
4.061-4.2076.320.26546.551999719997316331630.9660.11460.289699.9
3.931-4.0616.740.31825.872131221312316431640.9590.1320.344899.9
3.816-3.9316.890.36025.242179921799316531650.9620.14770.389899.7
3.715-3.8167.040.44484.512224722247316131610.9350.17980.480299.7
3.623-3.7157.080.52263.92241322413316631660.9150.21070.563999.6
3.539-3.6227.160.61523.332263222632316331630.8840.24610.663199.7
3.462-3.5397.20.70872.942276922769316431640.860.28270.763598.3
3.387-3.4627.220.83392.522285922859316431640.8420.33160.89894.3
3.312-3.3877.260.98472.232297222972316431640.7870.38941.059585
3.207-3.3127.111.02072.072249622496316331630.7550.40751.099865.9
2.927-3.2076.351.10671.642010620106316531650.6580.45991.200965.6

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Processing

Software
NameVersionClassification
autoPROC1.1.7 20200918data processing
XDSMar 15, 2019data reduction
XSCALEdata scaling
STARANISO2.3.46data scaling
BUSTER2.11.8refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.928→250.97 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.883 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.481
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 3075 -RANDOM
Rwork0.2282 ---
obs0.2293 63276 76 %-
Displacement parametersBiso mean: 78.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.5749 Å20 Å20 Å2
2---1.2373 Å20 Å2
3---1.8121 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: LAST / Resolution: 2.928→250.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24135 0 0 7 24142
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00948720HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0488251HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d14598SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes7790HARMONIC5
X-RAY DIFFRACTIONt_it24627HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion3150SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact34591SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion17.26
LS refinement shellResolution: 2.93→3.1 Å
RfactorNum. reflection% reflection
Rfree0.318 58 -
Rwork0.3275 --
obs0.3271 1266 9.51 %

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