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- PDB-3zlz: Lys6-linked tri-ubiquitin -

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Basic information

Entry
Database: PDB / ID: 3zlz
TitleLys6-linked tri-ubiquitin
ComponentsUBIQUITIN
KeywordsSIGNALING PROTEIN / ATYPICAL CHAIN TYPE / DEUBIQUITINASE / NLEL / BACTERIAL EFFECTOR
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail
Similarity search - Function
Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHospenthal, M.K. / Freund, S.M.V. / Komander, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Assembly, Analysis and Architecture of Atypical Ubiquitin Chains
Authors: Hospenthal, M.K. / Freund, S.M.V. / Komander, D.
History
DepositionFeb 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2May 22, 2013Group: Database references
Revision 1.3Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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)17,5377
Polymers17,2102
Non-polymers3275
Water00
1
A: UBIQUITIN
hetero molecules

A: UBIQUITIN
B: UBIQUITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,27210
Polymers25,8153
Non-polymers4587
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
identity operation1_555x,y,z1
2
A: UBIQUITIN
hetero molecules

A: UBIQUITIN
hetero molecules

A: UBIQUITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2079
Polymers25,8153
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
Buried area1890 Å2
ΔGint-203.1 kcal/mol
Surface area10120 Å2
MethodPISA
3
B: UBIQUITIN
hetero molecules

B: UBIQUITIN
hetero molecules

B: UBIQUITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,40312
Polymers25,8153
Non-polymers5899
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area2290 Å2
ΔGint-285.9 kcal/mol
Surface area10390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.930, 104.930, 104.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein UBIQUITIN


Mass: 8604.845 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: TRI-UBIQUITIN CHAIN LINKED VIA LYS6. K48R IN BOTH MOLECULES. ISOPEPTIDE LINKAGES ARE NOT RESOLVED.
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLACI / References: UniProt: P0CG47
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

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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: 2.83 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 7.4 / Details: 20% (V/V) PEG3350 AND 0.2 M ZINC ACETATE, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979192
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979192 Å / Relative weight: 1
ReflectionResolution: 2.9→74.2 Å / Num. obs: 4579 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 81.48 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.4
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W9N

2w9n


Resolution: 2.9→33.182 Å / SU ML: 0.42 / σ(F): 1.35 / Phase error: 31.77 / Stereochemistry target values: ML
Details: SOME LOOPS AND SIDE CHAINS ARE NOT MODELED DUE TO DISORDER. UBIQUITIN POLYMER, TWO UBIQUITINS IN ASYMMETRIC UNIT, AND THIRD UBIQUITIN THIRD UBIQUITIN IS PART OF NEIGHBOURING ASYMMETRIC UNIT.
RfactorNum. reflection% reflection
Rfree0.2882 578 12.78 %
Rwork0.2493 --
obs0.2542 4112 95.98 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.3 Å2
Refinement stepCycle: LAST / Resolution: 2.9→33.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1003 0 5 0 1008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021013
X-RAY DIFFRACTIONf_angle_d0.561387
X-RAY DIFFRACTIONf_dihedral_angle_d11.705339
X-RAY DIFFRACTIONf_chiral_restr0.034186
X-RAY DIFFRACTIONf_plane_restr0.002176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9002-3.19190.37661390.3398989X-RAY DIFFRACTION99
3.1919-3.65320.31181370.2605994X-RAY DIFFRACTION98
3.6532-4.60070.25821670.2136970X-RAY DIFFRACTION97
4.6007-33.18390.28621350.25071027X-RAY DIFFRACTION91
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)
15.90473.23741.06723.14823.54616.49690.00010.1472-0.195-0.1517-0.15570.24380.18340.1340.10010.7120.0726-0.08850.518-0.0070.6846-20.512211.275329.3624
26.7357-1.4295-0.3132.154-0.18296.0794-0.67770.01180.2701-0.13210.77060.0015-0.523-0.3697-0.12490.6437-0.0233-0.06080.63690.02270.4975-12.0073-1.18968.514
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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