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- PDB-3p45: Crystal structure of apo-caspase-6 at physiological pH -

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Basic information

Entry
Database: PDB / ID: 3p45
TitleCrystal structure of apo-caspase-6 at physiological pH
Components(caspase-6Caspase 6) x 2
KeywordsHYDROLASE / protease / Huntington's disease / mature apo-caspase-6 / physiological pH / competitive inhibition
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
Caspase-like / 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 ...Caspase-like / 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.53 Å
AuthorsMueller, I. / Lamers, M.B.A.C. / Ritchie, A.J. / Dominguez, C. / Munoz, I. / Maillard, M. / Kiselyov, A.
CitationJournal: To be Published
Title: Crystal structures of active and inhibitor-bound human Casp6
Authors: Mueller, I. / Lamers, M.B.A.C. / Ritchie, A.J. / Dominquez, C. / Munoz, I. / Maillard, M. / Kiselyov, A.
History
DepositionOct 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
E: caspase-6
F: caspase-6
G: caspase-6
H: caspase-6
I: caspase-6
J: caspase-6
K: caspase-6
L: caspase-6
M: caspase-6
N: caspase-6
O: caspase-6
P: caspase-6


Theoretical massNumber of molelcules
Total (without water)263,00416
Polymers263,00416
Non-polymers00
Water3,621201
1
A: caspase-6
B: caspase-6
C: caspase-6
D: caspase-6


Theoretical massNumber of molelcules
Total (without water)65,7514
Polymers65,7514
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8820 Å2
ΔGint-63 kcal/mol
Surface area17100 Å2
MethodPISA
2
E: caspase-6
F: caspase-6
G: caspase-6
H: caspase-6


Theoretical massNumber of molelcules
Total (without water)65,7514
Polymers65,7514
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-62 kcal/mol
Surface area17240 Å2
MethodPISA
3
I: caspase-6
J: caspase-6
K: caspase-6
L: caspase-6


Theoretical massNumber of molelcules
Total (without water)65,7514
Polymers65,7514
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-62 kcal/mol
Surface area17000 Å2
MethodPISA
4
M: caspase-6
N: caspase-6
O: caspase-6
P: caspase-6


Theoretical massNumber of molelcules
Total (without water)65,7514
Polymers65,7514
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-61 kcal/mol
Surface area17000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.230, 161.240, 88.920
Angle α, β, γ (deg.)90.000, 94.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
caspase-6 / Caspase 6


Mass: 20474.346 Da / Num. of mol.: 8 / Fragment: unp residues 1-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP6 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P55212
#2: Protein
caspase-6 / Caspase 6


Mass: 12401.176 Da / Num. of mol.: 8 / Fragment: unp residues 193-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP6 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P55212
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 3.3 M sodium nitrate, 0.1 M Tris, 0.5 % ethyl acetate, 5 mM THP, pH 7.4, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.53→29.958 Å / Num. all: 75818 / Num. obs: 75818 / % possible obs: 99.8 % / Redundancy: 2.9 % / Rsym value: 0.101 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.53-2.672.80.551.430684110300.5599.8
2.67-2.832.80.4091.229640104820.409100
2.83-3.022.90.262.92801298200.26100
3.02-3.272.90.1674.52633091640.167100
3.27-3.582.90.1053.72427084520.105100
3.58-42.90.0811.92203576370.081100
4-4.622.90.04813.41958267440.048100
4.62-5.662.90.04314.71655656900.04399.9
5.66-82.90.04713.81294444210.04799.5
8-29.9582.90.03216.4691723780.03297.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.95 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.6 Å29.11 Å
Translation2.6 Å29.11 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.53→29.958 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.884 / WRfactor Rfree: 0.2582 / WRfactor Rwork: 0.2047 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8316 / SU B: 21.529 / SU ML: 0.215 / SU R Cruickshank DPI: 0.4279 / SU Rfree: 0.2884 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 3815 5 %RANDOM
Rwork0.2072 ---
obs0.2101 75784 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 39.94 Å2 / Biso mean: 31.529 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å20.57 Å2
2---1.13 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.53→29.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12754 0 0 201 12955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02213041
X-RAY DIFFRACTIONr_bond_other_d0.0010.028941
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.94917551
X-RAY DIFFRACTIONr_angle_other_deg0.987321667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.14951576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.29223.193592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.055152240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0551572
X-RAY DIFFRACTIONr_chiral_restr0.1050.21933
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214318
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022863
X-RAY DIFFRACTIONr_mcbond_it0.6391.57957
X-RAY DIFFRACTIONr_mcbond_other0.1291.53259
X-RAY DIFFRACTIONr_mcangle_it1.234212704
X-RAY DIFFRACTIONr_scbond_it1.9835084
X-RAY DIFFRACTIONr_scangle_it3.2154.54847
LS refinement shellResolution: 2.53→2.596 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 264 -
Rwork0.337 5290 -
all-5554 -
obs--99.57 %
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)
12.6539-0.50720.16681.7412-1.15453.0081-0.079-0.0507-0.22680.12480.04890.1322-0.04120.0720.03010.1537-0.00610.00380.1662-0.0430.060431.811-40.024106.224
21.9942-1.1674-0.21864.02411.34774.0209-0.1987-0.0628-0.12230.2518-0.00220.52930.4010.12890.20090.20710.03050.12130.11960.10230.260633.354-68.405105.043
32.4867-0.13560.12941.7340.4394.28860.1493-0.0049-0.0327-0.1382-0.0495-0.1172-0.02760.3914-0.09970.1223-0.01970.00980.18070.02390.027839.668-37.33965.068
42.4107-0.67850.20293.2175-1.8493.53480.16340.0342-0.1272-0.39210.00980.41010.499-0.0156-0.17330.34850.0687-0.10340.1453-0.09290.163734.989-65.6563.66
51.8851-0.09490.50812.1467-0.34583.5997-0.07070.1181-0.0497-0.0790.09350.16940.03-0.064-0.02280.1147-0.03630.01190.14610.00380.024616.059-16.02622.237
62.85440.448-1.35582.1413-0.55362.8870.02930.39610.3309-0.07360.12880.3314-0.1604-0.3904-0.15810.1477-0.0302-0.13630.40410.09090.2672-12.284-14.0718.756
72.78980.3365-1.55352.84170.06533.43060.218-0.25540.19280.0863-0.16370.2915-0.25930.0774-0.05420.1722-0.0820.00640.161-0.03880.042311.22-11.70363.612
83.63241.39080.88361.6578-0.0063.12750.0963-0.23290.65890.1502-0.1540.3665-0.1374-0.22880.05770.1228-0.010.12610.3007-0.12870.3467-17.278-14.6260.59
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 163
2X-RAY DIFFRACTION1B198 - 291
3X-RAY DIFFRACTION2C31 - 162
4X-RAY DIFFRACTION2D200 - 291
5X-RAY DIFFRACTION3E31 - 162
6X-RAY DIFFRACTION3F202 - 292
7X-RAY DIFFRACTION4H200 - 291
8X-RAY DIFFRACTION4G32 - 162
9X-RAY DIFFRACTION5I31 - 163
10X-RAY DIFFRACTION5J201 - 292
11X-RAY DIFFRACTION6K31 - 163
12X-RAY DIFFRACTION6L202 - 291
13X-RAY DIFFRACTION7M31 - 163
14X-RAY DIFFRACTION7N202 - 292
15X-RAY DIFFRACTION8P201 - 292
16X-RAY DIFFRACTION8O31 - 162

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