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- PDB-5ld9: Structure of deubiquitinating enzyme homolog, Pyrococcus furiosus... -

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Basic information

Entry
Database: PDB / ID: 5ld9
TitleStructure of deubiquitinating enzyme homolog, Pyrococcus furiosus JAMM1.
ComponentsJAMM1
KeywordsHYDROLASE / JAMM/MPN+ / metalloprotease / isopeptidase / deubiquitination
Function / homology
Function and homology information


desampylase / metallopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
JAB domain, prokaryotic / Prokaryotic homologs of the JAB domain / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile.
Similarity search - Domain/homology
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.733 Å
AuthorsMaupin-Furlow, J.A. / Franzetti, B. / Cao, S. / Girard, E. / Gabel, F. / Engilberge, S.
Funding support France, United States, 4items
OrganizationGrant numberCountry
French National Research AgencyANR-13-BS07-0007-02 Ln23 France
French National Research AgencyANR-12-BSV8-0019-0 France
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM57498-15 United States
Department of Energy (DOE, United States)DE-FG02-05ER15650 United States
CitationJournal: Structure / Year: 2017
Title: Structural Insight into Ubiquitin-Like Protein Recognition and Oligomeric States of JAMM/MPN(+) Proteases.
Authors: Cao, S. / Engilberge, S. / Girard, E. / Gabel, F. / Franzetti, B. / Maupin-Furlow, J.A.
History
DepositionJun 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _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_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: JAMM1
B: JAMM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2445
Polymers32,0772
Non-polymers1663
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-98 kcal/mol
Surface area13110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.202, 37.147, 60.131
Angle α, β, γ (deg.)97.29, 104.18, 100.07
Int Tables number1
Space group name H-MP1

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Components

#1: Protein JAMM1


Mass: 16038.624 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Gene: PF1070 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1Y4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 65% methyl-2,4-pentanediol, 100 mM HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.28316, 1.28375, 1.28482
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.283161
21.283751
31.284821
ReflectionResolution: 1.73→35.99 Å / Num. obs: 27124 / % possible obs: 94 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 12.5
Reflection shellResolution: 1.73→1.84 Å / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.7 / Num. unique all: 8145

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.733→25.388 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 19.93
RfactorNum. reflection% reflection
Rfree0.1886 1357 5 %
Rwork0.1567 --
obs0.1583 27118 93.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.733→25.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 3 209 2267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052120
X-RAY DIFFRACTIONf_angle_d0.7382873
X-RAY DIFFRACTIONf_dihedral_angle_d17.7011312
X-RAY DIFFRACTIONf_chiral_restr0.057325
X-RAY DIFFRACTIONf_plane_restr0.005364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7331-1.7950.25911270.23112415X-RAY DIFFRACTION88
1.795-1.86690.24151340.18892542X-RAY DIFFRACTION93
1.8669-1.95180.24751360.18122585X-RAY DIFFRACTION93
1.9518-2.05460.19751340.15792545X-RAY DIFFRACTION94
2.0546-2.18330.15641390.14272637X-RAY DIFFRACTION95
2.1833-2.35180.19391340.13862551X-RAY DIFFRACTION95
2.3518-2.58820.18711380.15412625X-RAY DIFFRACTION95
2.5882-2.96230.17371380.16472607X-RAY DIFFRACTION95
2.9623-3.73020.20391400.14922663X-RAY DIFFRACTION96
3.7302-25.39070.1711370.15372591X-RAY DIFFRACTION94
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)
14.5037-4.41241.19174.3463-0.9292.4615-0.2793-0.9576-0.19850.37470.4018-0.09720.13630.2072-0.27250.2711-0.0114-0.03880.3145-0.0190.23530.8411-13.690683.4647
21.94170.21860.10562.34881.18664.65950.0154-0.0152-0.13630.1640.0153-0.05820.4538-0.1591-0.05530.23010.0234-0.04460.15640.01490.178129.3683-23.619374.6679
35.31634.6937-4.13544.1506-3.65373.2176-0.0990.293-0.83830.72490.1588-0.40182.0953-0.7745-0.06290.9075-0.119-0.03960.3445-0.0370.357223.4933-33.0673.0254
42.74221.65051.38113.05120.16680.97070.1641-0.476-0.79380.3290.13910.31061.3855-0.3696-0.15530.7267-0.07620.04660.32970.10630.355921.3655-29.279886.0606
55.2691-0.99080.14062.90050.45714.55950.14050.0768-0.0856-0.0301-0.0640.140.245-0.27-0.07750.132-0.0095-0.00490.12810.01020.164822.5554-17.904469.4238
62.1247-0.10110.80552.22550.45652.3182-0.13140.01690.1260.05430.03770.0934-0.0708-0.02460.08050.1736-0.00690.02420.15710.00530.238222.0299-10.811371.9098
73.3440.41033.22594.42410.2613.3815-0.3959-0.35990.33950.40950.2188-0.038-0.4396-0.17940.32050.15280.00980.02240.274-0.06130.289922.3975-8.233377.7636
84.68091.68782.60063.80281.89956.6560.03360.87850.056-0.27930.1774-0.2679-0.06021.1132-0.20570.23270.04160.05590.38990.02150.229522.7753-6.63441.2609
93.55121.25683.02721.88582.72335.7172-0.0770.02520.0539-0.0350.03470.0602-0.1826-0.05310.07520.2477-0.02300.17030.02820.181816.3615-1.525549.803
102.37983.12442.1086.73214.35463.2407-0.50410.30960.6165-0.115-0.24240.5837-0.8921-0.04380.82450.33880.0578-0.01560.3034-0.01850.29756.96795.443246.4659
112.4576-1.42010.37592.2033-1.29533.47150.1123-0.1633-0.0825-0.0531-0.0038-0.06990.26410.0688-0.12550.2217-0.0106-0.00190.1501-0.00550.187317.6169-9.59153.6498
122.43140.91070.65734.95420.02475.74450.3164-0.2896-0.4296-0.1803-0.03180.18190.417-0.1892-0.31930.24780.0176-0.0310.16620.00820.157617.7831-11.710950.6482
138.6820.9977-1.77874.7473-3.52633.1582-0.4021-0.4524-0.67171.4176-0.23760.38560.7184-0.37080.56010.9883-0.01670.23341.35170.22050.4487.5087-18.268756.4622
143.8779-0.2301-0.08174.8364-2.7345.89650.27440.2307-0.537-0.3496-0.0385-0.00880.92150.1813-0.43770.63070.0648-0.08440.258-0.06670.333815.789-17.861943.6419
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 12:22)
2X-RAY DIFFRACTION2(chain A and resid 23:62)
3X-RAY DIFFRACTION3(chain A and resid 63:69)
4X-RAY DIFFRACTION4(chain A and resid 70:85)
5X-RAY DIFFRACTION5(chain A and resid 86:116)
6X-RAY DIFFRACTION6(chain A and resid 117:130)
7X-RAY DIFFRACTION7(chain A and resid 131:140)
8X-RAY DIFFRACTION8(chain B and resid 12:32)
9X-RAY DIFFRACTION9(chain B and resid 33:65)
10X-RAY DIFFRACTION10(chain B and resid 66:80)
11X-RAY DIFFRACTION11(chain B and resid 81:105)
12X-RAY DIFFRACTION12(chain B and resid 106:125)
13X-RAY DIFFRACTION13(chain B and resid 126:130)
14X-RAY DIFFRACTION14(chain B and resid 131:140)

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