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- PDB-4l83: Structure of a putative Ubiquitin-conjugating enzyme E2 from Brug... -

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Basic information

Entry
Database: PDB / ID: 4l83
TitleStructure of a putative Ubiquitin-conjugating enzyme E2 from Brugia malayi
ComponentsUbe2i2 protein
KeywordsLIGASE / Ubiquitin / SSGCID / Seattle Structural Genomics Center for Infectious Disease / NIAID / National Institute of Allergy and Infectious Diseases / Ubiquitin-conjugating enzyme
Function / homologyUbiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Roll / Alpha Beta / :
Function and homology information
Biological speciesBrugia malayi (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Structure of a putative Ubiquitin-conjugating enzyme E2 from Brugia malayi
Authors: Clifton, M.C. / Edwards, T.E.
History
DepositionJun 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ube2i2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2602
Polymers20,1981
Non-polymers621
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.850, 52.030, 108.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-434-

HOH

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Components

#1: Protein Ube2i2 protein / Ubiquitin-conjugating enzyme E2


Mass: 20197.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brugia malayi (agent of lymphatic filariasis)
Gene: Bm1_40505 / Production host: Escherichia coli (E. coli) / References: UniProt: A8Q0Z3
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 28mg/ml BrmaA.00250.a, 200mM sodium malonate dibasic, 20% PEG3350, 20% ethylene glycol for cryoprotection. , pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 22536 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.511 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 19.48
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.740.4243.9289541665100
1.74-1.790.3485.294731579100
1.79-1.840.2666.6994221557100
1.84-1.90.2197.9790971499100
1.9-1.960.15910.9987991454100
1.96-2.030.13312.4685901415100
2.03-2.110.116.118297137199.9
2.11-2.190.08418.778019132199.9
2.19-2.290.07720.1776111260100
2.29-2.40.06622.3173941226100
2.4-2.530.05924.7169981158100
2.53-2.690.05327.2966791107100
2.69-2.870.04829.8461841037100
2.87-3.10.04333.17579097899.9
3.1-3.40.0435.65252897100
3.4-3.80.03837.664761833100
3.8-4.390.03739.194123737100
4.39-5.380.03638.73341462499.8
5.38-7.60.03837.47265851099.8
7.60.0435.67133430897.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.82 Å46.92 Å
Translation4.82 Å46.92 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GRN

2grn


Resolution: 1.7→46.97 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2034 / WRfactor Rwork: 0.17 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8832 / SU B: 3.304 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0975 / SU Rfree: 0.0989 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1152 5.1 %RANDOM
Rwork0.1702 ---
obs0.172 22499 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.88 Å2 / Biso mean: 21.6398 Å2 / Biso min: 11.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2---0.36 Å2-0 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1322 0 4 218 1544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191457
X-RAY DIFFRACTIONr_bond_other_d0.0010.021411
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.9641990
X-RAY DIFFRACTIONr_angle_other_deg0.75633266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7225190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06323.56273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06215261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3591514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211683
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02351
X-RAY DIFFRACTIONr_mcbond_it0.6661.055689
X-RAY DIFFRACTIONr_mcbond_other0.6641.052688
X-RAY DIFFRACTIONr_mcangle_it1.1331.577866
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 83 -
Rwork0.193 1579 -
all-1662 -
obs--99.94 %
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)
11.17720.8631-0.07923.1089-0.36210.9824-0.18590.1163-0.0532-0.37170.0967-0.07680.1118-0.02740.08920.1103-0.00670.00770.0735-0.01010.033513.19042.852611.0797
21.10441.2356-0.06842.1688-0.09310.52170.0261-0.08340.05940.0749-0.070.0518-0.02990.0140.04390.05510.00830.0040.0796-0.00050.069216.699711.701924.445
31.33080.41.21744.06154.64577.4273-0.02980.18340.0971-0.24640.08590.0014-0.13670.2879-0.05610.1076-0.0218-0.02010.07220.01990.042922.25818.26358.1718
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 68
2X-RAY DIFFRACTION2A69 - 145
3X-RAY DIFFRACTION3A146 - 168

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