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- PDB-4iyr: Crystal structure of full-length caspase-6 zymogen -

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Basic information

Entry
Database: PDB / ID: 4iyr
TitleCrystal structure of full-length caspase-6 zymogen
ComponentsCaspase-6
KeywordsHYDROLASE / caspase fold / protease
Function / homology
Function and homology information


caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / cellular response to staurosporine / positive regulation of necroptotic process / hepatocyte apoptotic process / Apoptotic cleavage of cellular proteins / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response / protein autoprocessing ...caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / cellular response to staurosporine / positive regulation of necroptotic process / hepatocyte apoptotic process / Apoptotic cleavage of cellular proteins / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response / protein autoprocessing / intrinsic apoptotic signaling pathway by p53 class mediator / Caspase-mediated cleavage of cytoskeletal proteins / epithelial cell differentiation / cysteine-type peptidase activity / activation of innate immune response / positive regulation of neuron apoptotic process / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / proteolysis / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Rossmann fold - #1460 / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues ...Rossmann fold - #1460 / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.697 Å
AuthorsCao, Q. / Wang, X.-J. / Li, L.-F. / Su, X.-D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The regulatory mechanism of the caspase 6 pro-domain revealed by crystal structure and biochemical assays.
Authors: Cao, Q. / Wang, X.J. / Li, L.F. / Su, X.D.
History
DepositionJan 29, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Caspase-6
B: Caspase-6


Theoretical massNumber of molelcules
Total (without water)69,3052
Polymers69,3052
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-19 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.062, 158.062, 126.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Caspase-6 / CASP-6 / Apoptotic protease Mch-2 / Caspase-6 subunit p18 / Caspase-6 subunit p11


Mass: 34652.438 Da / Num. of mol.: 2 / Mutation: H121A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP6 / Production host: Escherichia coli (E. coli) / References: UniProt: P55212, caspase-6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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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: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1M KH2PO4, 0.1M NaH2PO4, 0.1M Bis-tris, 1.75M NaCl, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.697→50 Å / Num. all: 22399 / Num. obs: 21861 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 50.69 Å2 / Rsym value: 0.088

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.automr: 1.6.1_357)model building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
SCALAdata scaling
PHENIX1.6.1_357phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NR2
Resolution: 2.697→33.545 Å / Occupancy max: 1 / Occupancy min: 0.98 / FOM work R set: 0.8487 / SU ML: 0.32 / σ(F): 1.33 / Phase error: 21.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 1116 5.13 %
Rwork0.18 --
obs0.1825 21743 96.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.328 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 159.73 Å2 / Biso mean: 48.8145 Å2 / Biso min: 16.24 Å2
Baniso -1Baniso -2Baniso -3
1--2.9376 Å2-0 Å20 Å2
2---2.9376 Å2-0 Å2
3---5.8751 Å2
Refinement stepCycle: LAST / Resolution: 2.697→33.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 0 21 3369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083423
X-RAY DIFFRACTIONf_angle_d1.1144630
X-RAY DIFFRACTIONf_chiral_restr0.076525
X-RAY DIFFRACTIONf_plane_restr0.004586
X-RAY DIFFRACTIONf_dihedral_angle_d13.4411181
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6971-2.81980.31781580.24282504266296
2.8198-2.96830.27431520.21562549270198
2.9683-3.15420.24471560.19622582273899
3.1542-3.39750.25781390.1832593273298
3.3975-3.7390.18371270.15362596272398
3.739-4.27910.18381320.14452588272097
4.2791-5.38760.18231280.14642612274097
5.3876-33.5480.26961240.21552603272792
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.9778-0.0583-0.05720.248-0.6121.7959-0.1062-0.2351-0.2740.1815-0.00580.04260.1093-0.2730.06930.1726-0.01770.05820.15730.04110.18740.7532-27.729752.4517
21.18860.4385-0.0471.8883-0.32171.263-0.02990.08070.1257-0.1008-0.08370.05670.095-0.2440.10530.12530.00540.00010.14170.00560.135-1.5993-21.725739.1884
31.35040.4003-0.69940.9581-0.15520.4841-0.14150.26220.2038-0.25860.1526-0.1274-0.10620.0987-0.070.21950.00580.09950.30620.01740.26319.6212-9.976728.897
41.59280.1632-0.56280.8307-0.03281.3858-0.1070.1218-0.4663-0.19320.0689-0.3105-0.00690.11470.06750.25130.02350.10350.2298-0.00280.309618.9352-24.165731.6622
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 32:173)A32 - 173
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 187:291)A187 - 291
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 32:163)B32 - 163
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 200:292)B200 - 292

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