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- PDB-1oi0: CRYSTAL STRUCTURE OF AF2198, A JAB1/MPN DOMAIN PROTEIN FROM ARCHA... -

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Basic information

Entry
Database: PDB / ID: 1oi0
TitleCRYSTAL STRUCTURE OF AF2198, A JAB1/MPN DOMAIN PROTEIN FROM ARCHAEOGLOBUS FULGIDUS
ComponentsHYPOTHETICAL PROTEIN AF2198
KeywordsHYDROLASE / PROTEASOME / DEUBIQUITINATION / ARCHAEA
Function / homology
Function and homology information


metallopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
JAB domain, prokaryotic / Prokaryotic homologs of the JAB domain / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / MPN domain / MPN domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / MPN domain-containing protein
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.5 Å
AuthorsTran, H.J.T.T. / Allen, M.D. / Lowe, J. / Bycroft, M.
CitationJournal: Biochemistry / Year: 2003
Title: The Structure of the Jab1/Mpn Domain and its Implications for Proteasome Function
Authors: Tran, H.J.T.T. / Allen, M.D. / Lowe, J. / Bycroft, M.
History
DepositionJun 4, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
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_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN AF2198
B: HYPOTHETICAL PROTEIN AF2198
C: HYPOTHETICAL PROTEIN AF2198
D: HYPOTHETICAL PROTEIN AF2198
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,97010
Polymers55,4644
Non-polymers5066
Water5,008278
1
A: HYPOTHETICAL PROTEIN AF2198
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0533
Polymers13,8661
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HYPOTHETICAL PROTEIN AF2198
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9312
Polymers13,8661
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: HYPOTHETICAL PROTEIN AF2198
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9312
Polymers13,8661
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: HYPOTHETICAL PROTEIN AF2198
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0533
Polymers13,8661
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)37.787, 87.081, 67.827
Angle α, β, γ (deg.)90.00, 94.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HYPOTHETICAL PROTEIN AF2198 / AF2198


Mass: 13865.925 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O28085
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsADDITIONAL RESIDUES NEEDED FOR CLONING/PROTEIN PURIFICATION

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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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growpH: 7.8
Details: 100MM MGCL2, 100MM TRIS (PH 7.8), 11% PEG 4000, 5 MM DTT
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
140 mg/mlprotein1drop
22 mMdithiothreitol1drop
310 mMTris-HCl1droppH7.0
411 %PEG40001reservoir
5100 mM1reservoirMgCl2
6100 mMTris-HCl1reservoirpH7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Details: RIGAKU
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. obs: 69516 / % possible obs: 85.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.4
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 3.8 / % possible all: 78.6
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 25 Å / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 78.6 % / Rmerge(I) obs: 0.338

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.5→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: DISORDERED REGIONS WERE NOT BUILT
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2954 5 %RANDOM
Rwork0.213 ---
obs0.213 59270 85.6 %-
Displacement parametersBiso mean: 24.98 Å2
Baniso -1Baniso -2Baniso -3
1--7.123 Å20 Å22.381 Å2
2--3.551 Å20 Å2
3---3.572 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 0 20 278 3679
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.395
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.5→1.51 Å / Num. reflection Rwork: 53 / Total num. of bins used: 50
Refinement
*PLUS
Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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