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- PDB-6mj9: CRYSTAL STRUCTURE OF UBIQUITIN-CONJUGATING ENZYME FROM NAEGLERIA ... -

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Basic information

Entry
Database: PDB / ID: 6mj9
TitleCRYSTAL STRUCTURE OF UBIQUITIN-CONJUGATING ENZYME FROM NAEGLERIA FOWLERI, APO FORM
ComponentsUbiquitin-conjugating enzyme
KeywordsPROTEIN BINDING / SSGCID / NAEGLERIA FOWLERI / UBIQUITIN-CONJUGATING ENZYME / E2 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


transferase activity / ATP binding
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF UBIQUITIN-CONJUGATING ENZYME FROM NAEGLERIA FOWLERI, APO FORM
Authors: Davies, D.R. / Dranow, D.M. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionSep 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.formula_weight / _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme


Theoretical massNumber of molelcules
Total (without water)19,3451
Polymers19,3451
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.300, 42.870, 89.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin-conjugating enzyme


Mass: 19344.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1W2VMZ9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 1.86 Å3/Da / Density % sol: 33.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MORPHEUS E9 (50 MM TRIS-HCL, 50 MM BICINE PH 8.5, 30 MM DIETHYLENE GLYCOL; 30 MM TRIETHYLENE GLYCOL; 30 MM TETRAETHYLENE GLYCOL; 30 MM PETAETHYLENE GLYCOL; 20% GLYCEROL; 10% PEG 4000, TRAY ...Details: MORPHEUS E9 (50 MM TRIS-HCL, 50 MM BICINE PH 8.5, 30 MM DIETHYLENE GLYCOL; 30 MM TRIETHYLENE GLYCOL; 30 MM TETRAETHYLENE GLYCOL; 30 MM PETAETHYLENE GLYCOL; 20% GLYCEROL; 10% PEG 4000, TRAY 303865 PUCK RBT2-03, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 13, 2018
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 12875 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.76 % / Biso Wilson estimate: 31.29 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 30.4
Reflection shellResolution: 1.85→1.9 Å / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.94 / Num. unique all: 5516 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.14RC2_3191refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V0R

5v0r


Resolution: 1.85→38.7 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.73
RfactorNum. reflection% reflection
Rfree0.222 1311 10.18 %
Rwork0.183 --
obs0.187 12875 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.55 Å2
Refinement stepCycle: LAST / Resolution: 1.85→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1116 0 0 114 1230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.92410.29761380.27141242X-RAY DIFFRACTION100
1.9241-2.01160.30241460.21521259X-RAY DIFFRACTION100
2.0116-2.11770.261430.19411277X-RAY DIFFRACTION100
2.1177-2.25030.24741380.20061257X-RAY DIFFRACTION100
2.2503-2.42410.27151400.19181269X-RAY DIFFRACTION100
2.4241-2.66790.26551350.19191308X-RAY DIFFRACTION100
2.6679-3.05390.25371540.20331268X-RAY DIFFRACTION100
3.0539-3.8470.20481600.16591293X-RAY DIFFRACTION100
3.847-38.70880.16251570.15831391X-RAY DIFFRACTION100
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)
16.29982.33213.61915.71410.34639.0265-0.14380.391-0.2579-0.52150.1148-0.4179-0.02640.51990.04590.2483-0.00190.08160.1279-0.02140.19561.7133-12.7538-21.8894
22.00951.17931.57572.46241.86714.0649-0.0870.0075-0.0371-0.02350.039-0.1041-0.032-0.04120.03670.1390.0040.00550.12230.03530.13790.3398-8.8299-7.875
30.82590.34961.1076.78274.3064.2395-0.0839-0.17340.0894-0.3937-0.10120.1966-1.1665-0.6320.20680.3130.07-0.04630.2728-0.0140.2813-7.1431-0.5297-15.9549
47.81462.32593.78217.0575.87175.4508-0.1503-0.1121-0.018-0.08830.1359-0.1035-0.65050.0785-0.0310.25960.01010.02830.16330.03240.16583.6684-1.0266-11.9719
57.70546.4095-7.01995.806-6.48617.27780.27290.5251.41080.13230.52571.1448-1.0287-1.1574-0.84050.35470.117-0.02240.3334-0.00520.4061-3.10226.5587-1.9756
68.6589-2.6994.31739.3202-1.24354.1079-0.2726-0.53820.180.23250.1185-0.0013-0.5767-0.11350.13530.23810.00040.03420.1855-0.03040.13364.44745.37827.3482
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 11 THROUGH 38 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 39 THROUGH 98 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 99 THROUGH 112 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 113 THROUGH 125 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 126 THROUGH 134 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 135 THROUGH 155 )

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