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- PDB-5v0r: Crystal structure of ubiquitin-conjugating enzyme from Naegleria ... -

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Basic information

Entry
Database: PDB / ID: 5v0r
TitleCrystal structure of ubiquitin-conjugating enzyme from Naegleria fowleri with modified Cys99
ComponentsUbiquitin-conjugating enzyme
KeywordsLIGASE / 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 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like ...: / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / 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 / molecular replacement / Resolution: 1.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of ubiquitin-conjugating enzyme from Naegleria fowleri with modified Cys99
Authors: Irwin, R.M. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionFeb 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4613
Polymers19,4011
Non-polymers602
Water4,306239
1
A: Ubiquitin-conjugating enzyme
hetero molecules

A: Ubiquitin-conjugating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9226
Polymers38,8022
Non-polymers1204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area2390 Å2
ΔGint-36 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.360, 85.240, 33.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-446-

HOH

21A-448-

HOH

31A-463-

HOH

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Components

#1: Protein Ubiquitin-conjugating enzyme / NafoA.00601.c


Mass: 19401.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Strain: ATCC 30863 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1W2VMZ9*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.06 Å3/Da / Density % sol: 40.46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Top96 C9 (100 mM Tris-HCl pH 8.5, 200 mM MgCl2, 25 % PEG 3350), cryo 15% ethylene glycol, apo, tray 286982 puck vxx6-11

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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: Jan 27, 2016
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→42.62 Å / Num. obs: 22634 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.822 % / Biso Wilson estimate: 15.26 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.027 / Rrim(I) all: 0.028 / Χ2: 1.046 / Net I/σ(I): 48.14 / Num. measured all: 244943 / Scaling rejects: 80
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.594.0350.1986.266428163615930.9660.22797.4
1.59-1.636.9660.1879.4111104160815940.9880.20199.1
1.63-1.687.7080.15911.1811994156415560.9930.1799.5
1.68-1.737.9450.12814.1512124152715260.9950.13799.9
1.73-1.798.350.10916.9712367148114810.9960.116100
1.79-1.858.6860.09120.9612404142814280.9980.096100
1.85-1.929.1670.0726.8912504136413640.9980.074100
1.92-29.510.05534.3912877135413540.9990.058100
2-2.099.930.0474212711128012800.9990.049100
2.09-2.1910.2520.04251.1312477121712170.9990.044100
2.19-2.3111.4160.03659.95134141176117510.03899.9
2.31-2.4512.7420.03470.27142071116111510.03599.9
2.45-2.6213.3410.03175.01140351052105210.033100
2.62-2.8314.2220.02983.111389597797710.03100
2.83-3.115.4850.02696.281412291291210.027100
3.1-3.4718.7180.024114.251542482482410.025100
3.47-420.2080.021129.611487373673610.021100
4-4.919.9230.019130.211271163863810.019100
4.9-6.9319.5980.019127.22989750650510.0299.8
6.93-42.6217.5080.016123.36537530830710.01699.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→42.62 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.191 2106 9.3 %
Rwork0.1561 20528 -
obs0.1592 22634 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.07 Å2 / Biso mean: 20.3808 Å2 / Biso min: 9.09 Å2
Refinement stepCycle: final / Resolution: 1.55→42.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1142 0 2 246 1390
Biso mean--15.79 32.44 -
Num. residues----146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051205
X-RAY DIFFRACTIONf_angle_d0.8891655
X-RAY DIFFRACTIONf_chiral_restr0.052186
X-RAY DIFFRACTIONf_plane_restr0.007216
X-RAY DIFFRACTIONf_dihedral_angle_d14.311742
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5499-1.5860.23811310.19641295142697
1.586-1.62560.23091170.1791346146399
1.6256-1.66960.2021470.17161338148599
1.6696-1.71870.18631530.169213291482100
1.7187-1.77420.19481460.16413521498100
1.7742-1.83760.2351580.175313311489100
1.8376-1.91120.17941270.168813621489100
1.9112-1.99820.20291400.162413691509100
1.9982-2.10350.18331490.149713491498100
2.1035-2.23530.1791540.147213661520100
2.2353-2.40790.18581370.145513761513100
2.4079-2.65020.1851310.156713791510100
2.6502-3.03360.17221370.154914081545100
3.0336-3.82160.17421290.145614201549100
3.8216-42.63610.20771500.154415081658100
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)
17.7442-0.95591.27412.9808-0.90673.63560.02680.45180.292-0.3356-0.1521-0.14260.02440.18370.12080.14840.01790.01160.08620.0110.11155.0225-2.2217-16.3882
22.00140.5808-0.05563.2162-0.30641.0329-0.12280.07680.0068-0.26810.06540.0436-0.0748-0.05020.07610.09620.00890.01140.06280.00180.0969-2.198-6.5492-9.2561
33.44270.36210.26832.91460.29881.1531-0.1328-0.0531-0.1954-0.092-0.05230.1080.0038-0.07470.19210.10850.00160.01250.09760.00150.1163-3.0621-8.6497-5.7289
42.63541.092-0.3711.70690.34050.41690.0214-0.16220.07880.2024-0.05720.0950.10890.0420.03260.1239-0.00340.00080.09920.02820.1021.2288-15.834-3.2418
54.26792.5747-4.86563.1293-2.05286.0387-0.03710.0815-0.0807-0.06230.0862-0.01750.348-0.2225-0.04870.1228-0.01090.00150.13480.02170.13963.971-21.4148-7.7198
62.29260.68011.54772.9137-0.16022.0047-0.1468-0.0689-0.00060.1050.11230.0116-0.1126-0.07990.04380.10980.03260.02230.12270.01650.10398.0933-13.2433-13.2355
74.02623.946-0.05017.7352-2.93636.4044-0.01670.3029-0.0964-0.67780.0493-0.1050.42280.3762-0.0760.12110.03250.02170.17560.00050.1925-4.8268-22.706-13.4517
88.3303-0.30581.1412.12222.43595.20260.2075-0.05240.1372-0.0394-0.10750.0470.0517-0.3726-0.09970.0968-0.02930.01730.12270.03060.1091-17.2789-24.9977-9.5279
93.78694.16632.74554.74993.34112.60840.2631-1.17531.04930.0278-0.23020.0494-0.3553-0.2712-0.01290.2815-0.01950.09250.3183-0.11730.3378-17.6477-15.6256-4.2937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 36 )A21 - 36
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 60 )A37 - 60
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 70 )A61 - 70
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 96 )A71 - 96
5X-RAY DIFFRACTION5chain 'A' and (resid 97 through 106 )A97 - 106
6X-RAY DIFFRACTION6chain 'A' and (resid 107 through 120 )A107 - 120
7X-RAY DIFFRACTION7chain 'A' and (resid 121 through 133 )A121 - 133
8X-RAY DIFFRACTION8chain 'A' and (resid 134 through 151 )A134 - 151
9X-RAY DIFFRACTION9chain 'A' and (resid 152 through 155 )A152 - 163

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