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- PDB-3d6h: Crystal structure of human caspase-1 with a naturally-occurring A... -

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Basic information

Entry
Database: PDB / ID: 3d6h
TitleCrystal structure of human caspase-1 with a naturally-occurring Asn263->Ser substitution in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK)
Components
  • Caspase-1
  • Caspase-1 precursor
  • N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide
KeywordsHYDROLASE/HYDROLASE INHIBITOR / catalytic domain / naturally-occurring mutation / Apoptosis / Hydrolase / Protease / Thiol protease / Zymogen / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


aldose 1-epimerase activity / galactose catabolic process via UDP-galactose / glucose metabolic process / carbohydrate binding / DNA damage response
Similarity search - Function
Aldose 1-/Glucose-6-phosphate 1-epimerase / Aldose 1-epimerase / Caspase-like / Rossmann fold - #1460 / Glycoside hydrolase-type carbohydrate-binding / Galactose mutarotase-like domain superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamide / Uncharacterized protein YphB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRosen-Wolff, A. / Roesler, J. / Romanowski, M.J.
CitationJournal: To be Published / Year: 2008
Title: Mutated, structurally altered caspase-1 with decreased enzymatic and increased RIP2-meditated inflammatory activity leads to a new type of periodic fever (ICE fever).
Authors: Rosen-Wolff, A. / Romanowski, M.J. / Ritter, L. / Flecks, S. / Quoos, N. / Gramatt, J. / Petzold, C. / Nguyen, H.D. / Gahr, M. / Roesler, J.
History
DepositionMay 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-1
B: Caspase-1 precursor
C: N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide


Theoretical massNumber of molelcules
Total (without water)30,8363
Polymers30,8363
Non-polymers00
Water3,243180
1
A: Caspase-1
B: Caspase-1 precursor
C: N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide

A: Caspase-1
B: Caspase-1 precursor
C: N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide


Theoretical massNumber of molelcules
Total (without water)61,6726
Polymers61,6726
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area18000 Å2
ΔGint-97 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.377, 63.377, 142.547
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-110-

HOH

DetailsDimer of the p20/p10 dimer

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Components

#1: Protein Caspase-1 / CASP-1 / Interleukin-1 beta convertase / IL-1BC / IL-1 beta-converting enzyme / ICE / Interleukin-1 ...CASP-1 / Interleukin-1 beta convertase / IL-1BC / IL-1 beta-converting enzyme / ICE / Interleukin-1 beta-converting enzyme / p45 / Caspase-1 subunit p20 / Caspase-1 subunit p10


Mass: 19974.010 Da / Num. of mol.: 1 / Fragment: Caspase-1 subunit p20 / Mutation: N263S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Plasmid: pRSET B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+ / References: UniProt: P29466, EC: 3.4.22.36
#2: Protein Caspase-1 precursor / CASP-1 / Interleukin-1 beta convertase / IL-1BC / IL-1 beta-converting enzyme / ICE / Interleukin-1 ...CASP-1 / Interleukin-1 beta convertase / IL-1BC / IL-1 beta-converting enzyme / ICE / Interleukin-1 beta-converting enzyme / p45 / Caspase-1 subunit p20 / Caspase-1 subunit p10


Mass: 10389.950 Da / Num. of mol.: 1 / Fragment: Caspase-1 subunit p10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Plasmid: pRSET B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+ / References: UniProt: P29466, EC: 3.4.22.36
#3: Protein/peptide N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide


Type: Peptide-like / Class: Inhibitor / Mass: 471.907 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: N-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Crystals obtained by hanging-drop vapor diffusion at 4 C (277K) against a reservoir of 0.1 M PIPES pH 6.0, 75-175 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3, and 2 mM MgCl2. All ...Details: Crystals obtained by hanging-drop vapor diffusion at 4 C (277K) against a reservoir of 0.1 M PIPES pH 6.0, 75-175 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3, and 2 mM MgCl2. All crystals cryoprotected in mother liquors supplemented with 20% (v/v) glycerol for 30-90 sec and immersion in liquid nitrogen. , VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 28, 2006
Details: Vertically collimating premirror, LN2 cooled double-crystal silicon (111) monochromator, toroidal focusing M2 mirror
RadiationMonochromator: iquid Nitrogen cooled Dual Crystal; crystal type S(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 19651 / % possible obs: 96.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 7.9
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 1.6 / % possible all: 87.4

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1sc3

1sc3


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.06 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23659 1011 5.1 %RANDOM
Rwork0.19987 ---
obs0.20174 18630 96.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.63 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å20 Å20 Å2
2---1.54 Å20 Å2
3---3.08 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 0 180 2236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222110
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.9682842
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8915252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30423.61794
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96815385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7641515
X-RAY DIFFRACTIONr_chiral_restr0.0820.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021561
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.2920
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21406
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2165
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6792.51322
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.90952070
X-RAY DIFFRACTIONr_scbond_it2.8982.5887
X-RAY DIFFRACTIONr_scangle_it4.3535772
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.069 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.271 81 -
Rwork0.206 1582 -
obs--86.57 %
Refinement TLS params.Method: refined / Origin x: 31.0324 Å / Origin y: 9.3696 Å / Origin z: 41.0698 Å
111213212223313233
T0.0791 Å20.0231 Å2-0.0419 Å2-0.0848 Å20.0435 Å2---0.1596 Å2
L22.3879 °22.688 °2-8.7156 °2-2.0494 °2-9.7047 °2--46.8092 °2
S1.1386 Å °2.2594 Å °-0.2678 Å °1.701 Å °0.3204 Å °0.3856 Å °-1.4271 Å °0.5024 Å °-1.4591 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B317
2X-RAY DIFFRACTION1A1

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