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- PDB-4gsw: Crystal structure of ubiquitin from Entamoeba histolytica to 2.15... -

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Basic information

Entry
Database: PDB / ID: 4gsw
TitleCrystal structure of ubiquitin from Entamoeba histolytica to 2.15 Angstrom
ComponentsUbiquitin
KeywordsPROTEIN BINDING / ubiquitin / ubiquitin-like modifier / ubiquitin fold / post-translational modification / EhUbc5 / EhUba1 / ubiquitination / isopeptide bond
Function / homology
Function and homology information


modification-dependent protein catabolic process / protein tag activity / protein ubiquitination / ubiquitin protein ligase binding
Similarity search - Function
Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily ...Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBosch, D.E. / Siderovski, D.P.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Determinants of Ubiquitin Conjugation in Entamoeba histolytica.
Authors: Bosch, D.E. / Siderovski, D.P.
History
DepositionAug 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Feb 13, 2013Group: Database references
Revision 1.3Sep 13, 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: Ubiquitin
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1574
Polymers17,9652
Non-polymers1922
Water79344
1
A: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1743
Polymers8,9821
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,9821
Polymers8,9821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.631, 49.865, 76.824
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 / / Ubiquitin / putative


Mass: 8982.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote)
Gene: EhUBI1, EHI_083270, EHI_083410, EHI_156660, EHI_178340
Plasmid: pLIC His / Production host: Escherichia coli (E. coli) / References: UniProt: C4M760
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 40.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: EhUbiquitin at 13 mg/mL in S200 buffer was mixed 1:1 with and equilibrated against crystallization solution containing 22% (w/v) PEG 3350, 200 mM LiSO4, and 100 mM Bis-Tris, pH 5.5, VAPOR ...Details: EhUbiquitin at 13 mg/mL in S200 buffer was mixed 1:1 with and equilibrated against crystallization solution containing 22% (w/v) PEG 3350, 200 mM LiSO4, and 100 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 8, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. all: 8593 / Num. obs: 8430 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 13.6
Reflection shellResolution: 2.15→2.17 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 3.1 / Num. unique all: 210 / % possible all: 96.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXAutoMRmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXAutoMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UBQ

1ubq


Resolution: 2.15→34.513 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 29.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 840 10.03 %RANDOM
Rwork0.1932 ---
obs0.1994 8379 97.53 %-
all-8591 --
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→34.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1165 0 10 44 1219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141192
X-RAY DIFFRACTIONf_angle_d1.4931606
X-RAY DIFFRACTIONf_dihedral_angle_d16.107470
X-RAY DIFFRACTIONf_chiral_restr0.094191
X-RAY DIFFRACTIONf_plane_restr0.007204
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.15-2.27720.35051290.26581154115492
2.2772-2.4530.34711350.2456121397
2.453-2.69970.33611410.2415126099
2.6997-3.09020.2711410.2206127699
3.0902-3.89240.26421450.1768129399
3.8924-34.51760.1931490.1598134398
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)
18.88254.2839-6.42947.5101-5.52087.7505-0.13630.0645-0.1283-0.5750.09030.49810.28890.11230.00820.3596-0.026-0.01210.3096-0.08560.4316-2.9252-17.067216.8572
28.73584.4651-1.00123.6026-2.17924.21650.1084-0.0855-0.0624-0.4293-0.1908-0.37670.0558-0.05220.04360.33240.0713-0.02590.2434-0.02330.4811-5.1492-8.057314.249
36.8637-5.00760.93687.13490.04183.50570.1044-0.21530.9020.453-0.01210.0763-0.19470.15020.00790.4440.0032-0.02670.2985-0.00850.465-5.512-7.009525.2201
46.0129-0.3649-3.39474.8498-0.0772.1587-0.0693-0.3594-0.0825-0.0779-0.1956-0.03860.06910.24660.25270.24230.0302-0.12380.29140.00470.35441.2656-9.278621.362
59.33616.6156-2.88015.9387-2.04633.07990.31540.1665-0.53050.7282-0.0346-1.32570.29010.3948-0.49720.4475-0.0134-0.08070.4096-0.030.395-11.35663.61421.4181
64.43232.33951.56562.1663.4679.09850.1158-0.07230.1625-0.1913-0.11210.0043-0.10420.03050.06830.29250.03410.01610.2180.02650.4959-10.10492.237812.3134
74.18181.6119-1.32735.30561.80394.8203-0.10590.0158-0.1921-0.2086-0.0002-0.03430.2476-0.76750.04390.34010.0264-0.09460.42270.07910.4536-22.1508-0.0988.1131
83.6481-0.3188-0.16834.82383.91093.26130.22740.2805-0.2308-0.25130.0457-0.7924-0.2597-0.7043-0.02810.40430.03070.01490.37960.08290.5466-17.04726.37415.4694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:18)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 19:37)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 38:55)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 56:75)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 4:23)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 24:44)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 45:64)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 65:76)

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