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- PDB-2m3x: Solution structure of Ph1500: a homohexameric protein centered on... -

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Basic information

Entry
Database: PDB / ID: 2m3x
TitleSolution structure of Ph1500: a homohexameric protein centered on a 12-bladed beta-propeller
ComponentsPH1500
KeywordsUNKNOWN FUNCTION / beta-propeller / 12-bladed / homohexamer / beta-clam
Function / homology
Function and homology information


Thrombin, subunit H - #360 / : / Domain of unknown function (DUF6849) / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / Thrombin, subunit H ...Thrombin, subunit H - #360 / : / Domain of unknown function (DUF6849) / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / Thrombin, subunit H / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CDC48 domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsVarnay, I. / Truffault, V. / Kessler, H. / Coles, M.
Citation
Journal: To be Published
Title: Solution structure of Ph1500: a homohexameric protein centered on a 12-bladed beta-propeller
Authors: Ammelburg, M. / Schiff, J. / Hartmann, M.D. / Varnay, I. / Djuranovic, S. / Truffault, V. / Martin, J. / Coles, M. / Lupas, A.N.
#2: Journal: J.Am.Chem.Soc. / Year: 2010
Title: Optimized measurement temperature gives access to the solution structure of a 49 kDa homohexameric -propeller
Authors: Varnay, I. / Truffault, V. / Djuranovic, S.D. / Ursinus, A. / Coles, M. / Kessler, H.
History
DepositionJan 28, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PH1500
B: PH1500
C: PH1500
D: PH1500
E: PH1500
F: PH1500


Theoretical massNumber of molelcules
Total (without water)100,3726
Polymers100,3726
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11488.1 Å2
ΔGint-70.6 kcal/mol
Surface area58289 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein
PH1500


Mass: 16728.738 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH1500 / Production host: Escherichia coli (E. coli) / References: UniProt: O59169

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1133D HNCO
1233D HN(CA)CB
1333D CBCA(CO)NH
1443D HNHA
1543D HNHB
1643D 1H-15N NOESY
1743D NNH-NOESY
1833D CNH-NOESY
1933D 1H-13C NOESY
11033D CCH-NOESY
11142D 15N-filtered 1H-1H NOESY
31223D trHNCO
31323D trHN(CA)CO
31423D trHNCA
31523D trHNCACB
21613D trHNCO
21713D trHNCA
21813D trHN(CA)CO
21913D HN(CA)HA
22013D (H)CCH-TOCSY
22113D (H)CCH-COSY
22213D (H)CCH-COSY
22332D 15N-filtered 1H-1H NOESY
22413D 1H-15N NOESY
22513D NNH-NOESY
22613D CNH-NOESY
22713D 1H-13C NOESY
22813D CCH-NOESY
22952D 1H-15N TROSY
23022D 1H-15N CRINEPT
13133D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-100% 13C; U-100% 15N] Ph1500C, 20 mM sodium phosphate, 250 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM [U-85% 2H; U-100% 13C; U-100% 15N] Ph1500C, 20 mM sodium phosphate, 250 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-100% 13C; U-100% 15N] Ph1500N, 50 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
41.0 mM [U-100% 15N] Ph1500N, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
50.6 mM [U-85% 2H; U-100% 13C; U-100% 15N] Ph1500, 20 mM sodium phosphate, 250 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMPh1500C-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
250 mMsodium chloride-31
0.6 mMPh1500C-4[U-85% 2H; U-100% 13C; U-100% 15N]2
20 mMsodium phosphate-52
250 mMsodium chloride-62
1.0 mMPh1500N-7[U-100% 13C; U-100% 15N]3
50 mMsodium phosphate-83
50 mMsodium chloride-93
1.0 mMPh1500N-10[U-100% 15N]4
20 mMsodium phosphate-114
50 mMsodium chloride-124
0.6 mMPh1500-13[U-85% 2H; U-100% 13C; U-100% 15N]5
20 mMsodium phosphate-145
250 mMsodium chloride-155
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1507ambient 300 K
22507.2ambient 353 K
32507.2ambient 318 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX7502
Bruker DMXBrukerDMX9003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.6Bruker Biospincollection
XwinNMR3.6Bruker Biospinprocessing
Sparky3.11Goddarddata analysis
X-PLOR NIH2.2.1Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.2.1Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Refinement is asymmetric. Each monomer has independent restraints and no symmetry operation is applied
NMR constraintsProtein chi angle constraints total count: 100 / Protein other angle constraints total count: 47 / Protein phi angle constraints total count: 131 / Protein psi angle constraints total count: 136
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.04 Å / Maximum torsion angle constraint violation: 0.4 ° / Maximum upper distance constraint violation: 0.14 Å
NMR ensemble rmsDistance rms dev: 0.0047 Å

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