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- PDB-6mfv: Crystal structure of the Signal Transduction ATPase with Numerous... -

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Basic information

Entry
Database: PDB / ID: 6mfv
TitleCrystal structure of the Signal Transduction ATPase with Numerous Domains (STAND) protein with a tetratricopeptide repeat sensor PH0952 from Pyrococcus horikoshii
Componentstetratricopeptide repeat sensor PH0952
KeywordsSIGNALING PROTEIN / STAND / nucleotide-binding oligomerization domain / tetratricopeptide / signal transduction
Function / homology
Function and homology information


ADP binding / DNA-binding transcription factor activity
Similarity search - Function
helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / : / ArsR-like helix-turn-helix domain / NB-ARC / NB-ARC domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats ...helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / : / ArsR-like helix-turn-helix domain / NB-ARC / NB-ARC domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Uncharacterized protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsLisa, M.N. / Alzari, P.M. / Haouz, A. / Danot, O.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-08-BLAN-0204-01 France
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Double autoinhibition mechanism of signal transduction ATPases with numerous domains (STAND) with a tetratricopeptide repeat sensor.
Authors: Lisa, M.N. / Cvirkaite-Krupovic, V. / Richet, E. / Andre-Leroux, G. / Alzari, P.M. / Haouz, A. / Danot, O.
History
DepositionSep 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 6, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Apr 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tetratricopeptide repeat sensor PH0952
B: tetratricopeptide repeat sensor PH0952
C: tetratricopeptide repeat sensor PH0952
D: tetratricopeptide repeat sensor PH0952
hetero molecules


Theoretical massNumber of molelcules
Total (without water)308,1228
Polymers306,4134
Non-polymers1,7094
Water00
1
A: tetratricopeptide repeat sensor PH0952
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0312
Polymers76,6031
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: tetratricopeptide repeat sensor PH0952
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0312
Polymers76,6031
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: tetratricopeptide repeat sensor PH0952
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0312
Polymers76,6031
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: tetratricopeptide repeat sensor PH0952
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0312
Polymers76,6031
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.126, 96.126, 584.259
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
tetratricopeptide repeat sensor PH0952


Mass: 76603.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH0952 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: O58663
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 10% (v/v) 2-propanol, 0.1 M imidazole pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.4→48.69 Å / Num. all: 241031 / Num. obs: 41809 / % possible obs: 100 % / Redundancy: 5.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.042 / Net I/σ(I): 8.9
Reflection shellResolution: 3.4→3.54 Å / Rmerge(I) obs: 0.791 / Num. unique all: 4743 / Num. unique obs: 27458 / CC1/2: 0.884 / Rpim(I) all: 0.355

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Obtained by SAD phasing

Resolution: 3.4→48.688 Å / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.89
RfactorNum. reflection% reflection
Rfree0.2716 4183 5.08 %
Rwork0.2244 --
obs0.2263 41668 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.4→48.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21276 0 108 0 21384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221884
X-RAY DIFFRACTIONf_angle_d0.48229488
X-RAY DIFFRACTIONf_dihedral_angle_d9.90213172
X-RAY DIFFRACTIONf_chiral_restr0.0383124
X-RAY DIFFRACTIONf_plane_restr0.0033748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.45860.32171830.28733931X-RAY DIFFRACTION95
3.4586-3.52150.35432000.28463951X-RAY DIFFRACTION94
3.5215-3.58920.27011930.28183882X-RAY DIFFRACTION95
3.5892-3.66240.34732060.28273879X-RAY DIFFRACTION94
3.6624-3.7420.33682420.27663907X-RAY DIFFRACTION94
3.742-3.8290.31532020.28293928X-RAY DIFFRACTION94
3.829-3.92460.28021820.27273917X-RAY DIFFRACTION95
3.9246-4.03070.27242290.26553980X-RAY DIFFRACTION94
4.0307-4.14920.29452300.25533866X-RAY DIFFRACTION94
4.1492-4.2830.29521770.24813916X-RAY DIFFRACTION95
4.283-4.43590.31211940.23453909X-RAY DIFFRACTION95
4.4359-4.61330.27282010.21883995X-RAY DIFFRACTION95
4.6133-4.82290.27922100.21133916X-RAY DIFFRACTION94
4.8229-5.07680.25131910.21933929X-RAY DIFFRACTION95
5.0768-5.39420.27522240.21533885X-RAY DIFFRACTION94
5.3942-5.80970.25862050.23363888X-RAY DIFFRACTION95
5.8097-6.39250.3022150.22463985X-RAY DIFFRACTION95
6.3925-7.31320.2292200.2033884X-RAY DIFFRACTION94
7.3132-9.19740.25572240.17043863X-RAY DIFFRACTION94
9.1974-41.62690.23052320.17473802X-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)
12.1813-0.9083-1.89534.7707-0.39835.73250.2567-0.59760.88760.3414-0.21130.0234-1.04910.2992-0.0761.16040.05330.07121.4838-0.4050.4086-99.126-33.3269-98.4847
20.31190.15410.43221.47940.71680.79290.8217-2.2423-0.76451.0062-0.57860.16861.04940.5906-0.20832.19580.23790.27862.38170.36760.8098-103.7596-50.8011-71.9295
38.4538-0.7871-3.09114.1579-5.10198.2133-0.27850.2356-0.4765-0.4034-0.24940.2723-0.4247-0.14130.59351.387-0.22330.27221.4631-0.43610.6317-117.939-34.9916-78.9926
43.35470.2786-1.66766.1822-1.28856.0114-1.1147-1.09631.0565-0.75080.15581.14390.5887-0.48590.53470.58950.1463-0.3161.3839-0.29481.5289-125.8953-22.2178-102.9832
52.5960.40730.39111.8506-1.9452.3799-0.5212-0.02141.9207-0.79310.58080.7719-0.4715-0.3611-0.03411.6076-0.0667-0.41841.0594-0.07351.5213-107.2088-5.394-123.7457
63.1453-2.56712.05434.7484-2.0633.0077-0.33670.5348-0.00170.43520.46270.75240.38640.6342-0.16380.51160.0887-0.31291.4410.12710.121-45.5782-39.2773-64.3242
71.2905-0.4582-0.82513.0305-0.72113.47470.5001-1.0306-0.3491-0.1421-0.062-0.7118-0.56461.53920.19421.63370.3555-0.95231.5545-0.14530.4251-29.3735-54.4091-41.006
86.9518-5.24860.95814.0737-1.44856.19431.2555-0.06120.24341.4099-1.0172-0.77021.2170.2724-0.03931.0638-0.3893-0.3310.61320.21960.855-50.0931-46.5117-38.2274
95.77180.291.37832.79491.80423.15470.196-0.1459-0.47610.7649-0.08530.67840.6475-0.99220.15730.27320.27810.23362.0269-0.1391.0254-72.9165-40.2747-53.9646
105.36261.4246-3.36113.3769-2.20952.62310.2080.19070.28870.00570.17250.4277-0.9126-0.3451-0.3551.091-0.0069-0.15570.8511-0.08260.5827-74.8235-19.3669-79.0527
112.27941.5962-2.31248.6295-5.97959.04160.0532-0.1753-0.3470.0033-0.16360.48380.09651.09440.09210.65640.11580.10331.5130.04260.2428-50.6867-48.7671-93.9718
126.1275.14914.77018.57353.41243.8065-0.4991.0850.1374-0.3790.5393-0.1495-0.07020.76840.11081.11110.18430.10241.3524-0.04590.3891-57.1837-31.0106-119.9774
136.10372.7816-0.68962.93943.11297.17870.94460.8211-0.91341.392-0.5879-1.42750.3958-0.419-0.31190.7809-0.1111-0.34991.60180.03320.9753-70.0941-47.929-113.0453
140.778-2.24190.26886.8006-0.16135.23440.5373-0.8873-0.87260.548-0.12931.18970.5146-1.1554-0.27311.0954-0.5385-0.06391.63490.36641.0174-76.4624-61.8452-89.1637
151.5796-2.07250.23653.3075-1.63312.13910.33720.5843-0.89830.19760.35920.78451.7192-0.2423-0.78391.75370.041-0.22151.1619-0.14551.211-56.0345-77.7061-69.3657
163.34681.4459-1.8674.5732-2.57092.16630.10460.0192-0.0025-0.20550.33921.6561-0.25581.1373-0.12881.2595-0.3572-0.17481.2858-0.2046-0.0708-93.685-43.2322-127.9835
171.67191.24562.55112.96140.59984.9166-0.00230.26310.1704-0.0572-0.1961-0.6511-0.86261.16550.1271.4584-0.8346-0.58991.30270.42170.9124-78.589-27.8214-151.9388
187.3663-0.9681-1.29237.94973.59456.45580.10940.34550.2737-0.7516-0.8244-1.3941-0.9416-0.9450.47321.369-0.6769-0.05171.04650.24230.7574-99.0843-36.4777-154.0849
193.87630.2325-5.08432.19981.75068.69690.05851.0733-0.4420.6674-0.64930.5281-0.5663-0.64650.49570.68120.1065-0.09240.5806-0.1530.924-121.2651-43.318-137.6924
202.0372-0.8480.99552.4517-3.4715.61630.3234-0.2035-0.43140.06060.09850.64860.7943-0.573-0.43831.0542-0.36570.09040.8156-0.15260.9411-121.8518-63.9604-112.2479
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 102 through 262 )
2X-RAY DIFFRACTION2chain 'A' and (resid 263 through 316 )
3X-RAY DIFFRACTION3chain 'A' and (resid 317 through 393 )
4X-RAY DIFFRACTION4chain 'A' and (resid 394 through 496 )
5X-RAY DIFFRACTION5chain 'A' and (resid 497 through 748 )
6X-RAY DIFFRACTION6chain 'B' and (resid 102 through 262 )
7X-RAY DIFFRACTION7chain 'B' and (resid 263 through 316 )
8X-RAY DIFFRACTION8chain 'B' and (resid 317 through 393 )
9X-RAY DIFFRACTION9chain 'B' and (resid 394 through 496 )
10X-RAY DIFFRACTION10chain 'B' and (resid 497 through 748 )
11X-RAY DIFFRACTION11chain 'C' and (resid 102 through 262 )
12X-RAY DIFFRACTION12chain 'C' and (resid 263 through 316 )
13X-RAY DIFFRACTION13chain 'C' and (resid 317 through 393 )
14X-RAY DIFFRACTION14chain 'C' and (resid 394 through 496 )
15X-RAY DIFFRACTION15chain 'C' and (resid 497 through 748 )
16X-RAY DIFFRACTION16chain 'D' and (resid 102 through 262 )
17X-RAY DIFFRACTION17chain 'D' and (resid 263 through 316 )
18X-RAY DIFFRACTION18chain 'D' and (resid 317 through 393 )
19X-RAY DIFFRACTION19chain 'D' and (resid 394 through 496 )
20X-RAY DIFFRACTION20chain 'D' and (resid 497 through 748 )

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