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

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Basic information

Entry
Database: PDB / ID: 9cqe
TitleCRYSTAL STRUCTURE OF APO C-TERMINAL HIS-TAG DOG HSP47(36-418) IN A P 1 21 1 CRYSTAL FORM
ComponentsSerpin H1
KeywordsCHAPERONE / SERPIN H1
Function / homology
Function and homology information


collagen trimer / collagen binding / serine-type endopeptidase inhibitor activity / endoplasmic reticulum lumen / 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: 3.177 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
Revision 1.1Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2024Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water00
1
A: Serpin H1


Theoretical massNumber of molelcules
Total (without water)44,2841
Polymers44,2841
Non-polymers00
Water0
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Serpin H1


Theoretical massNumber of molelcules
Total (without water)44,2841
Polymers44,2841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
F: Serpin H1


Theoretical massNumber of molelcules
Total (without water)44,2841
Polymers44,2841
Non-polymers00
Water0
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)140.18, 75.31, 163.87
Angle α, β, γ (deg.)90, 110.8, 90
Int Tables number4
Space group name H-MP1211

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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
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: 2.4 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 90 mM TRIS-HCL, pH 8.5, 22.5% (W/V) PEG 3350, 200 mM NON-DETERGENT SULFOBETAINE 221

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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 PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.177→153.193 Å / Num. obs: 39821 / % possible obs: 92.6 % / Redundancy: 3.39 % / CC1/2: 0.992 / CC1/2 anomalous: -0.177 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.112 / Rrim(I) all: 0.21 / AbsDiff over sigma anomalous: 0.814 / Baniso tensor eigenvalue 1: 68.3 Å2 / Baniso tensor eigenvalue 2: 71.9 Å2 / Baniso tensor eigenvalue 3: 134.2 Å2 / Baniso tensor eigenvector 1 ortho1: 0.9927 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0.121 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0.121 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 0.9927 / Aniso diffraction limit 1: 3.041 Å / Aniso diffraction limit 2: 2.647 Å / Aniso diffraction limit 3: 2.473 Å / Aniso diffraction limit axis 1 ortho1: 0.8277 / Aniso diffraction limit axis 1 ortho2: -0.41901 / Aniso diffraction limit axis 1 ortho3: 0.37328 / Aniso diffraction limit axis 2 ortho1: 0.48887 / Aniso diffraction limit axis 2 ortho2: 0.86497 / Aniso diffraction limit axis 2 ortho3: -0.11309 / Aniso diffraction limit axis 3 ortho1: -0.27551 / Aniso diffraction limit axis 3 ortho2: 0.27611 / Aniso diffraction limit axis 3 ortho3: 0.92079 / Net I/σ(I): 4.98 / Num. measured all: 133794 / Orthogonalization convention: pdb / % possible anomalous: 92.6 / % possible ellipsoidal: 92.6 / % possible ellipsoidal anomalous: 92.6 / % possible spherical: 73.1 / % possible spherical anomalous: 66.9 / Redundancy anomalous: 1.82
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
9.646-153.1933.120.05614.07660686068199019900.9942-0.45960.0370.0670.5180.83310.96320.83310.96320.83311.84
7.643-9.6463.340.06811.61665886588199219920.9956-0.47330.0430.0810.6730.91410.98860.91410.98860.91411.84
6.668-7.6433.460.1158.5168376837199119910.987-0.1830.0720.1360.7750.92230.9940.92230.9940.92231.87
6.056-6.6683.260.1726.26564256425199019900.9658-0.03870.1120.2060.8240.88320.9930.88320.9930.88321.78
5.614-6.0563.190.2095.29763076307199119910.9468-0.02990.140.2520.8460.86020.98860.86020.98860.86021.75
5.278-5.6143.330.2065.47265746574199219920.9545-0.00980.1320.2450.8640.91640.99150.91640.99150.91641.79
5.009-5.2783.420.2075.45367496749199119910.95170.02260.1310.2460.8530.92590.99350.92590.99350.92591.82
4.792-5.0093.460.1875.61168456845199119910.9719-0.04920.1180.2220.8070.9180.98860.9180.98860.9181.85
4.606-4.7923.480.1955.55668866886199119910.9702-0.07270.1220.2310.8080.91650.98960.91650.98960.91651.85
4.443-4.6063.520.2334.90769666966199019900.9558-0.00530.1450.2750.8240.93020.9920.93020.9920.93021.86
4.303-4.4433.290.2534.39365026502199219920.94240.01740.1660.3030.8550.86890.99350.86890.99350.86891.79
4.179-4.3033.360.2973.92166636663199219920.91810.03680.1910.3540.8310.9330.9940.9330.9940.9331.78
4.069-4.1793.440.3683.22468156815199119910.8925-0.04120.2320.4360.8180.92420.98560.92420.98560.92421.82
3.964-4.0693.210.4222.77463466346199019900.8292-0.00010.2810.5090.8680.83340.96650.83340.96650.83341.75
3.865-3.9643.350.4472.72566266626199119910.85630.06420.2870.5330.850.84810.91080.84810.89680.83771.77
3.763-3.8653.440.5282.46467936793199219920.823-0.00580.3310.6250.8420.8290.87680.8290.79430.75891.8
3.664-3.7633.490.5942.2168956895199019900.73520.03140.3680.70.870.83920.88920.83920.7260.69221.83
3.561-3.6643.50.6661.97569156915199119910.6650.030.4130.7850.8410.82860.88150.82860.63920.60681.83
3.448-3.5613.550.7731.68370287028199219920.6020.02150.4730.9080.8230.80240.84340.80240.50880.491.85
3.177-3.4483.510.9021.42669666966199119910.4991-0.0290.5591.0630.8350.53640.57240.53640.16930.15731.84

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata processing
XDSdata reduction
XSCALEdata scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.177→45.85 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.88 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.745
RfactorNum. reflection% reflectionSelection details
Rfree0.2882 2024 -RANDOM
Rwork0.2632 ---
obs0.2645 39803 73.1 %-
Displacement parametersBiso mean: 90.42 Å2
Baniso -1Baniso -2Baniso -3
1-2.7703 Å20 Å2-0.9584 Å2
2--1.7174 Å20 Å2
3----4.4877 Å2
Refine analyzeLuzzati coordinate error obs: 0.55 Å
Refinement stepCycle: LAST / Resolution: 3.177→45.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23196 0 0 0 23196
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00746240HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9383571HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d13784SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes7555HARMONIC5
X-RAY DIFFRACTIONt_it23660HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion3098SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact35411SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion16.29
LS refinement shellResolution: 3.18→3.36 Å
RfactorNum. reflection% reflection
Rfree0.3861 45 -
Rwork0.3299 --
obs0.3332 797 9.41 %

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