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- PDB-4d82: Metallosphera sedula Vps4 crystal structure -

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Basic information

Entry
Database: PDB / ID: 4d82
TitleMetallosphera sedula Vps4 crystal structure
ComponentsAAA ATPase, central domain proteinAAA proteins
KeywordsHYDROLASE
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding
Similarity search - Function
MIT (microtubule interacting and transport) domain / MIT domain superfamily / MIT domain / Microtubule Interacting and Trafficking molecule domain / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core ...MIT (microtubule interacting and transport) domain / MIT domain superfamily / MIT domain / Microtubule Interacting and Trafficking molecule domain / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / AAA ATPase, central domain protein / AAA ATPase, central domain protein
Similarity search - Component
Biological speciesMetallosphaera sedula (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsCaillat, C. / Macheboeuf, P. / Wu, Y. / McCarthy, A.A. / Boeri-Erba, E. / Effantin, G. / Gottlinger, H.G. / Weissenhorn, W. / Renesto, P.
CitationJournal: Nat.Commun. / Year: 2015
Title: Asymmetric Ring Structure of Vps4 Required for Escrt-III Disassembly.
Authors: Caillat, C. / Macheboeuf, P. / Wu, Y. / Mccarthy, A.A. / Boeri-Erba, E. / Effantin, G. / Gottlinger, H.G. / Weissenhorn, W. / Renesto, P.
History
DepositionDec 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref / struct_ref_seq / 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 / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _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: AAA ATPase, central domain protein
B: AAA ATPase, central domain protein
C: AAA ATPase, central domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1386
Polymers100,8563
Non-polymers1,2823
Water21612
1
A: AAA ATPase, central domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0462
Polymers33,6191
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AAA ATPase, central domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0462
Polymers33,6191
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: AAA ATPase, central domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0462
Polymers33,6191
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)151.187, 151.187, 98.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22B
13C
23B

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA97 - 36524 - 292
21CC97 - 36524 - 292
12AA97 - 36524 - 292
22BB97 - 36524 - 292
13CC90 - 36517 - 292
23BB90 - 36517 - 292

NCS ensembles :
ID
1
2
3

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Components

#1: Protein AAA ATPase, central domain protein / AAA proteins


Mass: 33618.715 Da / Num. of mol.: 3 / Fragment: AAA, UNP RESIDUES 75-369
Source method: isolated from a genetically manipulated source
Details: TRUNCATION OF THE RESIDUES 1-74 / Source: (gene. exp.) Metallosphaera sedula (archaea) / Gene: HA72_1672 / Plasmid: PDEST-17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: A0A088E656, UniProt: A4YHC5*PLUS
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.09 Å3/Da / Density % sol: 60.25 % / Description: NONE
Crystal growpH: 5.6
Details: 1,4 M SODIUM/POTASSIUM PHOSPHATE PH 5.6 (1.26 M SODIUM DIHYDROGEN PHOSPHATE MONOHYDRATE AND 0.14 M DI-POTASSIUM HYDROGEN PHOSPHATE) AND 7.5% (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.2→130.9 Å / Num. obs: 21217 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.9
Reflection shellResolution: 3.2→3.4 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D81

4d81


Resolution: 3.2→130.93 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.844 / SU B: 52.939 / SU ML: 0.419 / Cross valid method: THROUGHOUT / ESU R Free: 0.502 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26846 1081 5.1 %RANDOM
Rwork0.22755 ---
obs0.22961 20131 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.462 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å20.87 Å20 Å2
2--1.73 Å20 Å2
3----5.63 Å2
Refinement stepCycle: LAST / Resolution: 3.2→130.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6520 0 81 12 6613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196742
X-RAY DIFFRACTIONr_bond_other_d0.0040.026662
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.9949107
X-RAY DIFFRACTIONr_angle_other_deg1.094315376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5045809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40324.319301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.852151271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8521546
X-RAY DIFFRACTIONr_chiral_restr0.0770.21006
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217368
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021441
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9293.1163248
X-RAY DIFFRACTIONr_mcbond_other1.933.1163247
X-RAY DIFFRACTIONr_mcangle_it3.3444.6664050
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6353.2883494
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8664.8535056
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A164620.1
12C164620.1
21A167670.09
22B167670.09
31C166970.11
32B166970.11
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 93 -
Rwork0.291 1502 -
obs--99.63 %
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)
10.5155-0.5760.30113.4887-0.6461.21360.0686-0.01590.01470.2069-0.07760.1371-0.14670.05220.0090.10890.00270.02150.0184-0.02180.246325.316190.8430.485
22.5141-1.5137-0.73971.84160.81711.57630.14990.25630.07890.0137-0.0596-0.0087-0.0114-0.265-0.09040.0361-0.0103-00.17280.0780.3822-27.01248.087-37.13
33.5742-1.22820.50061.1833-0.02420.57470.00780.0447-0.20430.02050.02010.0354-0.0190.0082-0.02790.13550.0320.02870.01010.01710.2497-1.047204.594-16.572
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A97 - 366
2X-RAY DIFFRACTION2C90 - 366
3X-RAY DIFFRACTION3B88 - 366

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