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- PDB-5cw6: Structure of metal dependent enzyme DrBRCC36 -

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Basic information

Entry
Database: PDB / ID: 5cw6
TitleStructure of metal dependent enzyme DrBRCC36
ComponentsDrBRCC36
KeywordsMETAL BINDING PROTEIN / metalloprotease
Function / homology
Function and homology information


: / mitotic G2 DNA damage checkpoint signaling => GO:0007095 / : / BRISC complex / BRCA1-A complex / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / response to ionizing radiation / polyubiquitin modification-dependent protein binding / positive regulation of DNA repair / spindle pole ...: / mitotic G2 DNA damage checkpoint signaling => GO:0007095 / : / BRISC complex / BRCA1-A complex / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / response to ionizing radiation / polyubiquitin modification-dependent protein binding / positive regulation of DNA repair / spindle pole / metallopeptidase activity / double-strand break repair / cysteine-type deubiquitinase activity / cell cycle / cell division / metal ion binding / cytoplasm
Similarity search - Function
Brcc36 isopeptidase / BRCC36, C-terminal helical domain / BRCC36 C-terminal helical domain / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. ...Brcc36 isopeptidase / BRCC36, C-terminal helical domain / BRCC36 C-terminal helical domain / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Lys-63-specific deubiquitinase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.193 Å
AuthorsZeqiraj, E.
CitationJournal: Mol.Cell / Year: 2015
Title: Higher-Order Assembly of BRCC36-KIAA0157 Is Required for DUB Activity and Biological Function.
Authors: Zeqiraj, E. / Tian, L. / Piggott, C.A. / Pillon, M.C. / Duffy, N.M. / Ceccarelli, D.F. / Keszei, A.F. / Lorenzen, K. / Kurinov, I. / Orlicky, S. / Gish, G.D. / Heck, A.J. / Guarne, A. / ...Authors: Zeqiraj, E. / Tian, L. / Piggott, C.A. / Pillon, M.C. / Duffy, N.M. / Ceccarelli, D.F. / Keszei, A.F. / Lorenzen, K. / Kurinov, I. / Orlicky, S. / Gish, G.D. / Heck, A.J. / Guarne, A. / Greenberg, R.A. / Sicheri, F.
History
DepositionJul 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DrBRCC36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8462
Polymers29,7801
Non-polymers651
Water181
1
A: DrBRCC36
hetero molecules

A: DrBRCC36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6914
Polymers59,5602
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/31
Buried area2450 Å2
ΔGint-84 kcal/mol
Surface area15500 Å2
MethodPISA
2
A: DrBRCC36
hetero molecules

A: DrBRCC36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6914
Polymers59,5602
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area1970 Å2
ΔGint-85 kcal/mol
Surface area15990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.833, 108.833, 137.439
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein DrBRCC36


Mass: 29780.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0M3KL72*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.96 Å3/Da / Density % sol: 68.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.8 M succinic acid (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.193→50 Å / Num. obs: 8474 / % possible obs: 99.9 % / Redundancy: 10.1 % / Biso Wilson estimate: 84.46 Å2 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.074 / Rrim(I) all: 0.201 / Χ2: 0.98 / Net I/av σ(I): 12.667 / Net I/σ(I): 3.2 / Num. measured all: 85423
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.2-3.319.38160.8740.4640.87299.9
3.31-3.459.68180.8190.3290.8941000.976
3.45-3.610.38160.8620.2380.9111000.7320.771
3.6-3.7910.98290.9130.180.9371000.5690.598
3.79-4.0310.78390.9560.1210.9691000.380.399
4.03-4.3410.48250.9830.0851.0351000.2640.277
4.34-4.789.98480.9870.0551.14199.80.1660.175
4.78-5.4710.78550.9920.0531.0281000.1660.174
5.47-6.899.78710.9910.0480.99699.70.1450.154
6.89-509.49570.9990.0231.00399.80.0690.073

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.193→47.126 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 448 5.31 %Random selection
Rwork0.2139 7990 --
obs0.2154 8438 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.8 Å2 / Biso mean: 82.3258 Å2 / Biso min: 34.67 Å2
Refinement stepCycle: final / Resolution: 3.193→47.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1163 0 1 1 1165
Biso mean--78.89 34.67 -
Num. residues----151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021186
X-RAY DIFFRACTIONf_angle_d0.5271610
X-RAY DIFFRACTIONf_chiral_restr0.02191
X-RAY DIFFRACTIONf_plane_restr0.002202
X-RAY DIFFRACTIONf_dihedral_angle_d14.493413
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1934-3.65540.3081420.258225782720
3.6554-4.60480.22311410.201726312772
4.6048-47.13120.23051650.206527812946
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)
17.26551.45360.51077.8529-2.56277.3838-0.28460.6560.3933-0.93840.39030.1657-0.42270.0011-0.03090.6851-0.23370.04590.5928-0.16750.462848.4698-6.9587-18.3831
23.58562.31161.47216.85480.17695.5864-0.08220.2785-0.0275-0.59240.298-0.6170.26840.0512-0.30820.8765-0.13630.01320.6179-0.06520.363944.0195-15.4015-22.0385
33.0433-5.3477-0.86499.54520.21219.8069-0.19451.96020.8017-1.75540.0148-0.9834-1.27090.22530.18531.4621-0.47040.02141.03780.06850.727342.7988-13.1698-33.2752
44.4668-4.6879-4.9255.07295.18615.5048-0.28871.14820.2062-0.1040.0287-0.88070.6002-0.60420.12450.9249-0.2993-0.00410.7147-0.00390.534944.0319-14.5722-22.6343
59.81616.9818-2.29347.872-1.84428.99780.5544-0.57110.58870.2624-0.41471.4578-0.190.6488-0.5450.68160.0415-0.15620.4526-0.09850.74441.8604-1.9362-7.3197
61.9705-2.5708-2.37154.28894.03113.79960.1795-0.584-0.94810.4051-0.37480.51551.4507-1.43550.29610.9323-0.2479-0.02540.7883-0.00270.556434.6377-15.8283-11.5671
72.74971.54190.8966.31252.40474.33810.37320.0524-0.17740.738-0.3845-0.2449-0.2298-0.38550.03850.7253-0.0867-0.04550.5864-0.01790.369746.6054-7.2126-8.3504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 28 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 63 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 81 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 82 through 93 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 94 through 102 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 103 through 116 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 117 through 164 )A0

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