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- PDB-2wdp: Crystal Structure of Ligand Free Human Caspase-6 -

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Basic information

Entry
Database: PDB / ID: 2wdp
TitleCrystal Structure of Ligand Free Human Caspase-6
ComponentsCASPASE-6Caspase 6
KeywordsHYDROLASE / ALTERNATIVE SPLICING / ZYMOGEN / PROTEASE / APOPTOSIS / CYTOPLASM / POLYMORPHISM / THIOL PROTEASE / PHOSPHOPROTEIN
Function / homology
Function and homology information


caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / positive regulation of necroptotic process / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / cysteine-type endopeptidase activity involved in apoptotic process / hepatocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptosis ...caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / positive regulation of necroptotic process / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / cysteine-type endopeptidase activity involved in apoptotic process / hepatocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptosis / Apoptotic cleavage of cellular proteins / protein autoprocessing / intrinsic apoptotic signaling pathway by p53 class mediator / Caspase-mediated cleavage of cytoskeletal proteins / cysteine-type peptidase activity / epithelial cell differentiation / activation of innate immune response / 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 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 ...Rossmann fold - #1460 / 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
PHOSPHATE ION / Caspase-6
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBaumgartner, R. / Briand, C. / Meder, G. / Morse, R. / Renatus, M.
CitationJournal: Biochem.J. / Year: 2009
Title: The Crystal Structure of Caspase-6, a Selective Effector of Axonal Degeneration.
Authors: Baumgartner, R. / Meder, G. / Briand, C. / Decock, A. / D'Arcy, A. / Hassiepen, U. / Morse, R. / Renatus, M.
History
DepositionMar 25, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CASPASE-6
B: CASPASE-6
C: CASPASE-6
D: CASPASE-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,5315
Polymers133,4364
Non-polymers951
Water3,729207
1
A: CASPASE-6
B: CASPASE-6


Theoretical massNumber of molelcules
Total (without water)66,7182
Polymers66,7182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-24.6 kcal/mol
Surface area25700 Å2
MethodPQS
2
C: CASPASE-6
D: CASPASE-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8133
Polymers66,7182
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-27 kcal/mol
Surface area26840 Å2
MethodPQS
Unit cell
Length a, b, c (Å)63.146, 90.441, 86.397
Angle α, β, γ (deg.)90.00, 92.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 31:56 OR RESSEQ 58:92 OR RESSEQ...
211CHAIN B AND (RESSEQ 31:56 OR RESSEQ 58:92 OR RESSEQ...
311CHAIN C AND (RESSEQ 31:56 OR RESSEQ 58:92 OR RESSEQ...
411CHAIN D AND (RESSEQ 31:56 OR RESSEQ 58:92 OR RESSEQ...

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Components

#1: Protein
CASPASE-6 / Caspase 6 / APOPTOTIC PROTEASE MCH-2 / CASP-6


Mass: 33359.020 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P55212, caspase-6
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.37 Å3/Da / Density % sol: 48.13 % / Description: NONE
Crystal growpH: 6
Details: 1.5 M AMMONIUM CHLORIDE, 0.1 M SODIUM ACETATE AT PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.95→86.25 Å / Num. obs: 69153 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 25.52 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.6
Reflection shellHighest resolution: 1.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K86

1k86


Resolution: 1.95→63.072 Å / SU ML: 0.36 / σ(F): 1.37 / Phase error: 25.88 / Stereochemistry target values: ML
Details: DISORDERED RESIDUES CHAIN A 24-30 165-179 194-199 262-266 CHAIN B 24-30 165-179 194-197 262- -265 CHAIN C 24-30 165-179 CHAIN D 24-30 165-179
RfactorNum. reflection% reflection
Rfree0.262 3457 5 %
Rwork0.2243 --
obs0.2262 69145 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.377 Å2 / ksol: 0.395 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1667 Å20 Å2-0.0618 Å2
2---0.045 Å20 Å2
3---0.2117 Å2
Refinement stepCycle: LAST / Resolution: 1.95→63.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7327 0 5 207 7539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0177503
X-RAY DIFFRACTIONf_angle_d1.80510087
X-RAY DIFFRACTIONf_dihedral_angle_d17.8472729
X-RAY DIFFRACTIONf_chiral_restr0.1351073
X-RAY DIFFRACTIONf_plane_restr0.0091288
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1676X-RAY DIFFRACTIONPOSITIONAL
12B1676X-RAY DIFFRACTIONPOSITIONAL0.117
13C1676X-RAY DIFFRACTIONPOSITIONAL0.141
14D1676X-RAY DIFFRACTIONPOSITIONAL0.162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97670.32641340.252553X-RAY DIFFRACTION94
1.9767-2.0050.28661370.24922601X-RAY DIFFRACTION97
2.005-2.03490.30031370.23962603X-RAY DIFFRACTION97
2.0349-2.06670.261350.2372572X-RAY DIFFRACTION97
2.0667-2.10060.31051390.24162635X-RAY DIFFRACTION97
2.1006-2.13680.30591360.23552572X-RAY DIFFRACTION98
2.1368-2.17570.30841390.22792653X-RAY DIFFRACTION98
2.1757-2.21750.28481370.22412597X-RAY DIFFRACTION98
2.2175-2.26280.27891380.21372626X-RAY DIFFRACTION98
2.2628-2.3120.25841360.22472590X-RAY DIFFRACTION98
2.312-2.36580.29681390.21482636X-RAY DIFFRACTION98
2.3658-2.42490.2591390.21192630X-RAY DIFFRACTION98
2.4249-2.49050.2611380.21652632X-RAY DIFFRACTION98
2.4905-2.56380.30311380.2282626X-RAY DIFFRACTION98
2.5638-2.64650.27661380.22892626X-RAY DIFFRACTION98
2.6465-2.74110.27411400.22412651X-RAY DIFFRACTION98
2.7411-2.85090.2781380.22522621X-RAY DIFFRACTION98
2.8509-2.98060.26831400.22712662X-RAY DIFFRACTION98
2.9806-3.13770.25451380.21992619X-RAY DIFFRACTION98
3.1377-3.33430.27421400.22322656X-RAY DIFFRACTION98
3.3343-3.59170.26781390.222645X-RAY DIFFRACTION99
3.5917-3.95320.22911400.21512659X-RAY DIFFRACTION98
3.9532-4.5250.21991390.20472651X-RAY DIFFRACTION98
4.525-5.70050.21561410.21342676X-RAY DIFFRACTION98
5.7005-63.10520.24041420.23372696X-RAY DIFFRACTION98
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0101-0.19390.03350.40040.13650.1326-0.05360.0185-0.1150.0063-0.0655-0.26060.08260.1033-0.03660.05880.06230.01780.11960.03230.15023.7749-17.4725-43.3493
20.217-0.3365-0.03741.86120.5237-0.19590.2634-0.2147-0.2322-0.40440.0086-1.2369-0.3973-0.21640.3598-0.1828-0.1693-0.18480.19860.07340.647212.1638-8.3424-37.389
30.5829-0.40920.09780.30290.53730.6546-0.141-0.22740.11310.17270.03110.00920.04310.0455-0.01050.08190.06160.00410.13190.00380.1207-0.9483-11.4543-34.4393
41.0766-0.37790.37410.39470.4395-0.00060.0707-0.0424-0.1903-0.01340.03140.17360.03040.01580.16310.05830.0149-0.00340.07320.00470.1447-8.6856-18.6152-46.6416
51.0232-0.07230.45410.1905-0.38890.49450.13750.03610.01550.320.16680.493-1.0667-0.09910.2824-0.66320.1829-0.14850.172-0.01740.1281-31.44710.621-42.9866
60.02840.0503-0.05290.0208-0.0720.00360.0764-0.14530.275-0.0562-0.27920.27840.01880.14830.0010.0863-0.0880.13880.8082-0.10230.9658-40.4549-9.1992-36.8937
70.3649-0.06830.0310.0796-0.17090.1591-0.1711-0.1596-0.20320.15350.10830.1434-0.0295-0.35970.00070.1750.06620.02090.1917-0.02390.1467-27.3174-3.2178-32.4487
81.1798-0.7943-0.48630.81950.18210.17230.0570.05790.1341-0.05910.02270.0059-0.0917-0.04230.12120.05260.0196-0.01430.0909-0.0070.1155-19.9946-0.5103-44.5036
90.6263-0.64910.98060.5110.13221.02850.07040.0844-0.2201-0.0826-0.0823-0.09170.12590.3094-0.00010.33360.11060.07570.22730.00320.1924-0.1506-23.1023.4848
10-0.012-0.03780.030.0116-0.05380.02330.21130.1382-0.45580.38130.1627-0.17380.3188-0.24650.0010.2469-0.02960.00690.1508-0.1710.367-6.5218-33.8979-2.1552
110.3587-0.49640.27630.3219-0.01110.60030.15270.36150.2874-0.1891-0.01750.072-0.10520.31320.0020.28160.07530.0210.21330.01950.16-6.6063-17.6028-4.0509
120.4365-0.64740.12370.46720.54530.7442-0.0101-0.00260.08460.00650.0294-0.0617-0.04880.16480.00010.20260.01640.01250.15520.0290.1057-3.0679-9.83029.4345
130.4253-0.6716-0.63840.6451-0.59530.50130.00560.0484-0.00580.03350.0790.0893-0.0804-0.3082-00.19290.0649-0.02040.23380.02510.1421-29.7353.38984.3012
14-0.0245-0.0030.0523-0.04170.0368-0.0212-0.27720.2950.2483-0.0811-0.00920.0365-0.262-0.15870.00250.45870.1642-0.1960.45830.04180.4853-26.682915.6728-5.6344
150.4053-0.37350.06670.3684-0.40870.98030.17980.2171-0.0751-0.0726-0.0498-0.05170.4075-0.4626-0.00270.20870.0752-0.00880.13750.00280.1139-22.3298-0.0832-2.6624
160.7373-0.0669-0.09710.1886-0.33750.37560.0469-0.1939-0.10330.19860.03460.02020.069-0.0547-0.00020.1818-0.00530.02270.12020.01480.1563-28.0348-10.22088.6946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 31:91
2X-RAY DIFFRACTION2CHAIN A AND RESID 92:113
3X-RAY DIFFRACTION3CHAIN A AND RESID 114:202
4X-RAY DIFFRACTION4CHAIN A AND RESID 203:293
5X-RAY DIFFRACTION5CHAIN B AND RESID 31:92
6X-RAY DIFFRACTION6CHAIN B AND RESID 93:111
7X-RAY DIFFRACTION7CHAIN B AND RESID 112:145
8X-RAY DIFFRACTION8CHAIN B AND RESID 146:293
9X-RAY DIFFRACTION9CHAIN C AND RESID 31:92
10X-RAY DIFFRACTION10CHAIN C AND RESID 93:113
11X-RAY DIFFRACTION11CHAIN C AND RESID 114:221
12X-RAY DIFFRACTION12CHAIN C AND RESID 222:293
13X-RAY DIFFRACTION13CHAIN D AND RESID 31:91
14X-RAY DIFFRACTION14CHAIN D AND RESID 92:106
15X-RAY DIFFRACTION15CHAIN D AND RESID 107:221
16X-RAY DIFFRACTION16CHAIN D AND RESID 222:293

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