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- PDB-2bkq: NEDD8 protease -

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Basic information

Entry
Database: PDB / ID: 2bkq
TitleNEDD8 protease
ComponentsSENTRIN-SPECIFIC PROTEASE 8
KeywordsHYDROLASE / UBIQUITIN / PROTEASE / THIOL PROTEASE / UBL CONJUGATION PATHWAY / UBIQUITIN-HYDROLASE COMPLEX
Function / homology
Function and homology information


deNEDDylase activity / protein deneddylation / protein deubiquitination / cysteine-type peptidase activity / post-translational protein modification / UCH proteinases / Neddylation / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / cytosol
Similarity search - Function
NEDD8-specific protease 1/2-like / Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Papain-like cysteine peptidase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sentrin-specific protease 8
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShen, L.N. / Liu, H. / Dong, C. / Xirodimas, D. / Naismith, J.H. / Hay, R.T.
CitationJournal: Embo J. / Year: 2005
Title: Structural Basis of Nedd8 Ubiquitin Discrimination by the Deneddylating Enzyme Nedp1
Authors: Shen, L.N. / Liu, H. / Dong, C. / Xirodimas, D. / Naismith, J.H. / Hay, R.T.
History
DepositionFeb 18, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 9, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf ..._exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SENTRIN-SPECIFIC PROTEASE 8
B: SENTRIN-SPECIFIC PROTEASE 8
C: SENTRIN-SPECIFIC PROTEASE 8
D: SENTRIN-SPECIFIC PROTEASE 8


Theoretical massNumber of molelcules
Total (without water)96,2934
Polymers96,2934
Non-polymers00
Water6,954386
1
A: SENTRIN-SPECIFIC PROTEASE 8


Theoretical massNumber of molelcules
Total (without water)24,0731
Polymers24,0731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SENTRIN-SPECIFIC PROTEASE 8


Theoretical massNumber of molelcules
Total (without water)24,0731
Polymers24,0731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SENTRIN-SPECIFIC PROTEASE 8


Theoretical massNumber of molelcules
Total (without water)24,0731
Polymers24,0731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SENTRIN-SPECIFIC PROTEASE 8


Theoretical massNumber of molelcules
Total (without water)24,0731
Polymers24,0731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.070, 57.510, 74.996
Angle α, β, γ (deg.)99.74, 110.95, 92.41
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALASNASNAA4 - 914 - 91
21VALVALASNASNBB4 - 914 - 91
31VALVALASNASNCC4 - 914 - 91
41VALVALASNASNDD4 - 914 - 91
12SERSERPHEPHEAA104 - 139104 - 139
22SERSERPHEPHEBB104 - 139104 - 139
32SERSERPHEPHECC104 - 139104 - 139
42SERSERPHEPHEDD104 - 139104 - 139
13ALAALALEULEUAA148 - 209148 - 209
23ALAALALEULEUBB148 - 209148 - 209
33ALAALALEULEUCC148 - 209148 - 209
43ALAALALEULEUDD148 - 209148 - 209

NCS oper:
IDCodeMatrixVector
1given(0.383772, -0.801294, -0.458963), (0.567896, 0.596718, -0.56694), (0.728158, -0.043068, 0.684055)-2.1687, 45.4319, 34.409
2given(0.829165, 0.422811, -0.365672), (-0.554109, 0.708042, -0.437768), (0.073818, 0.565604, 0.821367)29.0528, 18.0891, 1.1508
3given(0.054373, -0.997135, 0.052591), (0.981682, 0.04375, -0.185437), (0.182605, 0.06171, 0.981248)38.4872, 16.5687, 37.4909

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Components

#1: Protein
SENTRIN-SPECIFIC PROTEASE 8 / SENTRIN/SUMO-SPECIFIC PROTEASE SENP8 / CYSTEINE PROTEASE FKSG8 / PROTEASE / CYSTEINE 2 / NEDP1


Mass: 24073.164 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) / Strain (production host): BL21(DE3)
References: UniProt: Q96LD8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: INVOLVED IN THE RELEASE OF SENTRINS (POTENTIAL)

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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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 9
Details: NEDP1 (14MG/ML) WITH EQUAL VOLUME OF RESERVOIR SOLUTION CONTAINING 0.1M BICINE PH9.0, 30% PEG3000., pH 9.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→67 Å / Num. obs: 54875 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→69.01 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.735 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2882 5 %RANDOM
Rwork0.193 ---
obs0.196 54258 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.72 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å21.47 Å20.99 Å2
2---1.51 Å20.57 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 2→69.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6631 0 0 386 7017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0216795
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9289222
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0355826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97525.074337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.303151106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4531521
X-RAY DIFFRACTIONr_chiral_restr0.1120.21008
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025241
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.23361
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.24743
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2489
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.2103
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8571.54254
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.43426719
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.38632861
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4294.52503
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A744medium positional0.430.5
2B744medium positional0.410.5
3C744medium positional0.440.5
4D744medium positional0.60.5
1A745loose positional0.855
2B745loose positional0.795
3C745loose positional0.785
4D745loose positional1.195
1A744medium thermal2.112
2B744medium thermal1.742
3C744medium thermal1.642
4D744medium thermal1.372
1A745loose thermal3.4110
2B745loose thermal2.9410
3C745loose thermal2.510
4D745loose thermal2.6610
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.291 201
Rwork0.216 3971
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)
10.9476-0.2125-0.36140.81230.0532.0136-0.02050.0499-0.063-0.09190.0146-0.05110.1609-0.0050.0058-0.054-0.07870.019-0.0127-0.0163-0.1474-0.32-0.016-0.398
21.1582-0.1332-0.45271.2276-0.56712.5859-0.0719-0.04420.02020.0439-0.0631-0.19950.03360.34030.135-0.0012-0.01410.00970.0007-0.0056-0.1225-2.50545.79834.568
32.3517-0.08440.62481.6071-0.09691.2749-0.08960.0820.3062-0.0372-0.01210.1222-0.177-0.04520.1017-0.0068-0.0538-0.01210.0058-0.0061-0.087528.83917.7431.07
40.77350.28280.18041.92560.27561.77210.0107-0.0466-0.09040.2995-0.00750.2234-0.1049-0.2921-0.00330.07320.0230.0702-0.0060.0098-0.13838.59616.80337.215
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 211
2X-RAY DIFFRACTION2B1 - 211
3X-RAY DIFFRACTION3C1 - 211
4X-RAY DIFFRACTION4D1 - 211

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