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- PDB-3kpa: Ubiquitin fold modifier conjugating enzyme from Leishmania major ... -

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Basic information

Entry
Database: PDB / ID: 3kpa
TitleUbiquitin fold modifier conjugating enzyme from Leishmania major (probable)
Componentsprobable Ubiquitin fold modifier conjugating enzyme
KeywordsLIGASE / UBL CONJUGATION PATHWAY / Structural Genomics / PSI / Structural Genomics of Pathogenic Protozoa Consortium / SGPP / Protein Structure Initiative
Function / homology
Function and homology information


UFM1 conjugating enzyme activity / UFM1 transferase activity / protein ufmylation / reticulophagy / response to endoplasmic reticulum stress
Similarity search - Function
Ubiquitin-fold modifier-conjugating enzyme 1 / Ubiquitin-fold modifier-conjugating enzyme 1 / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-fold modifier-conjugating enzyme 1
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsHan, G.W. / Le Trong, I. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be Published
Title: Ubiquitin fold modifier conjugating enzyme from Leishmania major (probable)
Authors: Merritt, E.A. / Le Trong, I. / Han, G.W. / Anderson, L. / Napuli, A. / Van Voorhis, W.C. / Buckner, F.S. / Fan, E. / Zucker, F. / Verlinde, L.M.J. / Hol, W.G.J.
History
DepositionNov 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: probable Ubiquitin fold modifier conjugating enzyme
B: probable Ubiquitin fold modifier conjugating enzyme
C: probable Ubiquitin fold modifier conjugating enzyme


Theoretical massNumber of molelcules
Total (without water)59,4293
Polymers59,4293
Non-polymers00
Water73941
1
A: probable Ubiquitin fold modifier conjugating enzyme


Theoretical massNumber of molelcules
Total (without water)19,8101
Polymers19,8101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: probable Ubiquitin fold modifier conjugating enzyme


Theoretical massNumber of molelcules
Total (without water)19,8101
Polymers19,8101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: probable Ubiquitin fold modifier conjugating enzyme


Theoretical massNumber of molelcules
Total (without water)19,8101
Polymers19,8101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.274, 34.133, 126.774
Angle α, β, γ (deg.)90.000, 99.320, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein probable Ubiquitin fold modifier conjugating enzyme


Mass: 19809.695 Da / Num. of mol.: 3 / Mutation: I152M
Source method: isolated from a genetically manipulated source
Details: uncleaved / Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LmjF15.1250 / Plasmid: PET14B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 STAR / References: UniProt: Q4QF57
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 40.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: protein buffer 25 mM HEPES pH 7.5, 120 mM NaCl; crystallization buffer 100 mM Na Cacodylate, 300 mM Ammonium Sulfate,, 30% PEG 4000, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9784 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2003
RadiationProtocol: MAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 23133 / Num. obs: 23133 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.4
Reflection shellResolution: 2.2→2.37 Å / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1776 / % possible all: 70.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2in1

2in1
PDB Unreleased entry


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.272 / WRfactor Rwork: 0.212 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.788 / SU B: 16.939 / SU ML: 0.195 / SU R Cruickshank DPI: 0.384 / SU Rfree: 0.264 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.384 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1187 5.1 %RANDOM
Rwork0.214 ---
obs0.217 23096 91.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 32.14 Å2 / Biso mean: 12.42 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20 Å20.54 Å2
2---0.45 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3828 0 0 41 3869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223967
X-RAY DIFFRACTIONr_bond_other_d0.0010.022738
X-RAY DIFFRACTIONr_angle_refined_deg1.221.9525405
X-RAY DIFFRACTIONr_angle_other_deg0.82636659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3595470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80223.314172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09115639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4691517
X-RAY DIFFRACTIONr_chiral_restr0.0710.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214339
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02828
X-RAY DIFFRACTIONr_mcbond_it0.4251.52361
X-RAY DIFFRACTIONr_mcbond_other0.0891.5934
X-RAY DIFFRACTIONr_mcangle_it0.80423831
X-RAY DIFFRACTIONr_scbond_it1.34731606
X-RAY DIFFRACTIONr_scangle_it2.1244.51573
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 77 -
Rwork0.243 1236 -
all-1313 -
obs--70.25 %
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)
113.8386-4.2022-2.58148.53581.57214.85070.0737-0.16950.7261-0.1083-0.17150.0784-0.3222-0.28560.09780.3458-0.0060.00070.08030.00210.085716.2016.5159.126
21.1382-0.03551.06052.58670.1072.72270.2436-0.13890.03790.0094-0.17660.19960.2182-0.311-0.0670.2915-0.00020.04090.0707-0.00150.075510.819-2.48660.089
32.36681.00551.35864.4201-0.43292.96710.06270.1242-0.0247-0.5788-0.04140.41840.1145-0.2777-0.02130.42020.0639-0.08270.2249-0.03140.18636.352-2.12745.532
42.79130.4740.95092.81381.05172.8866-0.0150.12920.1451-0.5207-0.13610.6556-0.3058-0.56220.15110.39920.0901-0.07230.197-0.01740.21763.293.8147.824
55.93081.35420.96016.35310.01015.59060.035-0.09640.5397-0.0198-0.20610.0942-0.2904-0.01070.17110.42070.00830.0750.0096-0.01410.0904-0.52216.8133.429
63.86191.51723.77595.38381.34414.6050.04430.07460.08480.0371-0.1214-0.39010.31840.3970.07720.34980.06160.0580.12740.01080.07987.3268.3338.234
72.0411-1.35641.66684.2372-0.30554.8665-0.2654-0.1670.01330.72260.1209-0.20760.088-0.01030.14440.48860.03390.02250.16470.03510.15473.6449.39921.123
83.0432-1.75670.78363.9118-2.33982.2329-0.3911-0.39180.22430.7880.1663-0.5682-0.67770.3010.22480.55840.0244-0.02490.2479-0.05160.21525.64917.52919.821
98.0332-1.65523.16395.2679-5.020919.63760.43370.64410.1511-0.507-0.3011-0.12830.2134-0.0489-0.13260.53760.03540.18330.3024-0.11630.1659-13.9228.317.45
105.39290.3081-5.58432.1191-1.554710.7095-0.40370.7217-0.7306-0.2501-0.16780.02840.3376-0.91910.57160.48030.07030.1280.267-0.12710.2942-22.99923.30824.634
1111.16963.9188-7.72644.3115-0.23197.84270.47920.05490.1244-0.1293-0.1543-0.227-0.8758-0.2808-0.32490.58620.19220.08720.2492-0.00510.257-24.32334.54634.495
127.65520.5334-11.51490.94880.223418.59450.0455-0.6324-0.1791-0.01390.0024-0.1676-0.29080.9509-0.04780.43210.1660.14870.2950.07210.2239-20.05727.32234.447
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 28
2X-RAY DIFFRACTION2A29 - 62
3X-RAY DIFFRACTION3A63 - 121
4X-RAY DIFFRACTION4A122 - 160
5X-RAY DIFFRACTION5B3 - 39
6X-RAY DIFFRACTION6B40 - 63
7X-RAY DIFFRACTION7B64 - 117
8X-RAY DIFFRACTION8B118 - 160
9X-RAY DIFFRACTION9C3 - 28
10X-RAY DIFFRACTION10C29 - 96
11X-RAY DIFFRACTION11C97 - 124
12X-RAY DIFFRACTION12C125 - 160

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