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- PDB-2w2u: STRUCTURAL INSIGHT INTO THE INTERACTION BETWEEN ARCHAEAL ESCRT-II... -

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Basic information

Entry
Database: PDB / ID: 2w2u
TitleSTRUCTURAL INSIGHT INTO THE INTERACTION BETWEEN ARCHAEAL ESCRT-III AND AAA-ATPASE
Components
  • CONSERVED ARCHAEAL PROTEIN
  • HYPOTHETICAL P60 KATANIN
KeywordsHYDROLASE/TRANSPORT / HYDROLASE TRANSPORT COMPLEX / NUCLEOTIDE-BINDING / ESCRT / AAA-ATPASE / CYTOKINESIS / ATP-BINDING / HYDROLASE-TRANSPORT complex
Function / homology
Function and homology information


nucleoid / cell division / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
: / : / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT (microtubule interacting and transport) domain / MIT domain superfamily / MIT domain / Microtubule Interacting and Trafficking molecule domain / : / AAA ATPase, AAA+ lid domain / AAA+ lid domain ...: / : / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT (microtubule interacting and transport) domain / MIT domain superfamily / MIT domain / Microtubule Interacting and Trafficking molecule domain / : / AAA ATPase, AAA+ lid domain / AAA+ lid domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Cell division protein B / AAA family ATPase
Similarity search - Component
Biological speciesSULFOLOBUS ACIDOCALDARIUS (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsObita, T. / Samson, R.Y. / Perisic, O. / Freund, S.M. / Bell, S.D. / Williams, R.L.
CitationJournal: Science / Year: 2008
Title: A Role for the Escrt System in Cell Division in Archaea.
Authors: Samson, R.Y. / Obita, T. / Freund, S.M. / Williams, R.L. / Bell, S.D.
History
DepositionNov 4, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2009Provider: 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 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYPOTHETICAL P60 KATANIN
B: HYPOTHETICAL P60 KATANIN
C: CONSERVED ARCHAEAL PROTEIN
D: CONSERVED ARCHAEAL PROTEIN


Theoretical massNumber of molelcules
Total (without water)22,4524
Polymers22,4524
Non-polymers00
Water2,126118
1
A: HYPOTHETICAL P60 KATANIN
C: CONSERVED ARCHAEAL PROTEIN


Theoretical massNumber of molelcules
Total (without water)11,2262
Polymers11,2262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-10.5 kcal/mol
Surface area6380 Å2
MethodPQS
2
B: HYPOTHETICAL P60 KATANIN
D: CONSERVED ARCHAEAL PROTEIN


Theoretical massNumber of molelcules
Total (without water)11,2262
Polymers11,2262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-11 kcal/mol
Surface area6250 Å2
MethodPQS
Unit cell
Length a, b, c (Å)49.855, 49.855, 107.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.282, -0.959, 0.001), (-0.959, -0.282, 0.005), (-0.004, -0.002, -1)0.04613, -0.20977, 71.51723
2given(0.362, -0.93, 0.056), (-0.927, -0.366, -0.08), (0.095, -0.023, -0.995)-3.80712, 3.45521, 69.15543

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Components

#1: Protein HYPOTHETICAL P60 KATANIN / SACI1372 / AAA FAMILY ATPASE


Mass: 9611.070 Da / Num. of mol.: 2 / Fragment: MIT DOMAIN, RESIDUES 1-75
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS ACIDOCALDARIUS (acidophilic)
Plasmid: POPTH / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 RIPL / References: UniProt: Q877H3
#2: Protein/peptide CONSERVED ARCHAEAL PROTEIN / SACI1373


Mass: 1614.838 Da / Num. of mol.: 2 / Fragment: RESIDUES 182-195 / Source method: obtained synthetically / Source: (synth.) SULFOLOBUS ACIDOCALDARIUS (acidophilic) / References: UniProt: Q4J924
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 10

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 7 / Details: 15% PEG4K, 0.1M TRIS(PH7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→49.88 Å / Num. obs: 12626 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 16.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.7 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V6Y

2v6y


Resolution: 2.2→49.88 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.876 / SU B: 5.188 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 679 5.1 %RANDOM
Rwork0.225 ---
obs0.227 12626 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2--0.53 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1370 0 0 118 1488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221386
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0432.0021864
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.755167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.3952564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47415275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.021510
X-RAY DIFFRACTIONr_chiral_restr0.0670.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021010
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.2714
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2910.2957
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2100
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5081.5899
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.70621374
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2523562
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1074.5490
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.263 53
Rwork0.225 932

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