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- PDB-5ubv: ATPase domain of i-AAA protease from Myceliophthora thermophila -

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Basic information

Entry
Database: PDB / ID: 5ubv
TitleATPase domain of i-AAA protease from Myceliophthora thermophila
ComponentsATPase domain of i-AAA protease
KeywordsHYDROLASE / AAA+ / protease / ATPase / mitochondria
Function / homology
Function and homology information


metalloendopeptidase activity / membrane => GO:0016020 / ATP binding
Similarity search - Function
Peptidase M41 / Peptidase, FtsH / Peptidase M41-like / Peptidase family M41 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core ...Peptidase M41 / Peptidase, FtsH / Peptidase M41-like / Peptidase family M41 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / CITRIC ACID / AAA domain-containing protein
Similarity search - Component
Biological speciesMyceliophthora thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsShi, H. / Glynn, S.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115898 United States
CitationJournal: To Be Published
Title: Structure of the ATPase domain of i-AAA protease from Myceliophthora thermophila
Authors: Shi, H. / Glynn, S.E.
History
DepositionDec 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATPase domain of i-AAA protease
B: ATPase domain of i-AAA protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3946
Polymers53,2552
Non-polymers1,1394
Water1,04558
1
A: ATPase domain of i-AAA protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2473
Polymers26,6271
Non-polymers6192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ATPase domain of i-AAA protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1473
Polymers26,6271
Non-polymers5192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.916, 86.624, 155.025
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 2:3 or resseq 5:10 or resseq...
21(chain B and (resseq 2:3 or resseq 5:10 or resseq...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNALAALA(chain A and (resseq 2:3 or resseq 5:10 or resseq...AA2 - 32 - 3
12PHEPHEGLYGLY(chain A and (resseq 2:3 or resseq 5:10 or resseq...AA5 - 105 - 10
13ASPASPVALVAL(chain A and (resseq 2:3 or resseq 5:10 or resseq...AA12 - 2212 - 22
14PHEPHEPHEPHE(chain A and (resseq 2:3 or resseq 5:10 or resseq...AA2424
15SERSERGLYGLY(chain A and (resseq 2:3 or resseq 5:10 or resseq...AA1 - 2461 - 246
16SERSERGLYGLY(chain A and (resseq 2:3 or resseq 5:10 or resseq...AA1 - 2461 - 246
17SERSERGLYGLY(chain A and (resseq 2:3 or resseq 5:10 or resseq...AA1 - 2461 - 246
18SERSERGLYGLY(chain A and (resseq 2:3 or resseq 5:10 or resseq...AA1 - 2461 - 246
19SERSERGLYGLY(chain A and (resseq 2:3 or resseq 5:10 or resseq...AA1 - 2461 - 246
110SERSERGLYGLY(chain A and (resseq 2:3 or resseq 5:10 or resseq...AA1 - 2461 - 246
111SERSERGLYGLY(chain A and (resseq 2:3 or resseq 5:10 or resseq...AA1 - 2461 - 246
112SERSERGLYGLY(chain A and (resseq 2:3 or resseq 5:10 or resseq...AA1 - 2461 - 246
21ASNASNALAALA(chain B and (resseq 2:3 or resseq 5:10 or resseq...BB2 - 32 - 3
22PHEPHEGLYGLY(chain B and (resseq 2:3 or resseq 5:10 or resseq...BB5 - 105 - 10
23ASPASPVALVAL(chain B and (resseq 2:3 or resseq 5:10 or resseq...BB12 - 2212 - 22
24PHEPHEPHEPHE(chain B and (resseq 2:3 or resseq 5:10 or resseq...BB2424
25ASNASNMETMET(chain B and (resseq 2:3 or resseq 5:10 or resseq...BB2 - 2452 - 245
26ASNASNMETMET(chain B and (resseq 2:3 or resseq 5:10 or resseq...BB2 - 2452 - 245
27ASNASNMETMET(chain B and (resseq 2:3 or resseq 5:10 or resseq...BB2 - 2452 - 245
28ASNASNMETMET(chain B and (resseq 2:3 or resseq 5:10 or resseq...BB2 - 2452 - 245
29ASNASNMETMET(chain B and (resseq 2:3 or resseq 5:10 or resseq...BB2 - 2452 - 245
210ASNASNMETMET(chain B and (resseq 2:3 or resseq 5:10 or resseq...BB2 - 2452 - 245
211ASNASNMETMET(chain B and (resseq 2:3 or resseq 5:10 or resseq...BB2 - 2452 - 245
212ASNASNMETMET(chain B and (resseq 2:3 or resseq 5:10 or resseq...BB2 - 2452 - 245

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Components

#1: Protein ATPase domain of i-AAA protease


Mass: 26627.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799) (fungus)
Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_2311706 / Production host: Escherichia coli (E. coli) / References: UniProt: G2QPI5
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.89 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.2 M Ammonium Citrate, 14% PEG 3350, 5 mM ADP, 5 mM Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Si (111) double crystal
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 23565 / % possible obs: 100 % / Redundancy: 9.2 % / Biso Wilson estimate: 47.63 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.032 / Rrim(I) all: 0.099 / Χ2: 1.113 / Net I/σ(I): 7.5 / Num. measured all: 216406
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.45-2.4981.0250.7691100
2.49-2.548.60.9590.831100
2.54-2.599.10.7780.8661100
2.59-2.649.40.7140.8971100
2.64-2.79.30.5590.9191100
2.7-2.769.50.50.9421100
2.76-2.839.40.380.9611100
2.83-2.99.50.3530.971100
2.9-2.999.50.270.9821100
2.99-3.099.40.240.9861100
3.09-3.29.40.1830.9921100
3.2-3.329.40.1490.9931100
3.32-3.489.40.1170.9961100
3.48-3.669.40.0830.9981100
3.66-3.899.30.0660.9981100
3.89-4.199.30.0580.9981100
4.19-4.619.30.0540.9981100
4.61-5.289.20.0450.9991100
5.28-6.659.10.0450.9991100
6.65-508.40.02711100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PHENIX1.10.1_2155phasing
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LV7

1lv7


Resolution: 2.45→44.378 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.66
RfactorNum. reflection% reflection
Rfree0.2376 1211 5.15 %
Rwork0.1964 --
obs0.1986 23503 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.54 Å2 / Biso mean: 60.7417 Å2 / Biso min: 25.16 Å2
Refinement stepCycle: final / Resolution: 2.45→44.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3646 0 73 58 3777
Biso mean--64.03 59.41 -
Num. residues----482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023790
X-RAY DIFFRACTIONf_angle_d0.4365118
X-RAY DIFFRACTIONf_chiral_restr0.038573
X-RAY DIFFRACTIONf_plane_restr0.003691
X-RAY DIFFRACTIONf_dihedral_angle_d8.9022304
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1807X-RAY DIFFRACTION5.745TORSIONAL
12B1807X-RAY DIFFRACTION5.745TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4497-2.54770.31341280.28772423255199
2.5477-2.66370.32951360.259324062542100
2.6637-2.80410.25081390.24124432582100
2.8041-2.97970.27491340.234224262560100
2.9797-3.20970.28541220.236424662588100
3.2097-3.53260.25951460.212424772623100
3.5326-4.04350.21491280.186424652593100
4.0435-5.09320.21891390.157625482687100
5.0932-44.38570.19871390.170926382777100
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)
16.109-0.1053-2.24845.2363-1.22455.6545-0.17260.2161-0.39760.27720.0873-0.23310.5195-0.15080.08290.4288-0.0007-0.07040.32680.04070.283527.510.876100.0612
23.9347-1.5804-2.44393.09711.89994.3653-0.0289-0.26920.51070.48970.0615-0.1388-0.1367-0.1638-0.00910.48020.0459-0.090.34670.01440.315521.782526.3194105.4147
31.32821.08580.58812.4719-1.11475.5014-0.0240.2163-0.0529-0.09070.1411-0.3210.13890.1963-0.11240.1703-0.0140.01360.4561-0.03720.361840.881918.857876.3462
46.3291-1.4698-0.17352.7318-0.071.9493-0.2436-0.70710.73390.37630.08890.3771-0.6042-0.34390.19360.73570.1149-0.10560.4224-0.17670.567339.976350.9819108.0395
53.3891-1.65020.0586.07942.69317.05460.12410.43060.1024-0.1855-0.19140.0986-0.08010.21520.02260.40180.0225-0.0470.3136-0.02380.298344.578938.499293.6586
63.70891.18693.33813.67511.13917.6305-0.62940.55970.6053-0.40090.22420.1797-1.25450.37190.36860.6983-0.0509-0.08540.41620.04380.409947.916349.543395.5001
75.37820.13410.41634.6627-3.2854.2687-0.2147-0.3168-0.36180.65760.1990.13750.0334-0.2710.03760.75240.0613-0.10120.3224-0.04620.321655.139936.0432127.065
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 63 )A1 - 63
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 174 )A64 - 174
3X-RAY DIFFRACTION3chain 'A' and (resid 175 through 246 )A175 - 246
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 63 )B2 - 63
5X-RAY DIFFRACTION5chain 'B' and (resid 64 through 123 )B64 - 123
6X-RAY DIFFRACTION6chain 'B' and (resid 124 through 174 )B124 - 174
7X-RAY DIFFRACTION7chain 'B' and (resid 175 through 245 )B175 - 245

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