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- PDB-2m08: The solution structure of NmPin, the parvuline of Nitrosopumilus ... -

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Basic information

Entry
Database: PDB / ID: 2m08
TitleThe solution structure of NmPin, the parvuline of Nitrosopumilus maritimus
ComponentsPpiC-type peptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / parvulin / archaeal / membrane / Thaumarchaeota / sdPar
Function / homologyPpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / peptidyl-prolyl cis-trans isomerase activity / Roll / Alpha Beta / PpiC-type peptidyl-prolyl cis-trans isomerase
Function and homology information
Biological speciesNitrosopumilus maritimus (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsLederer, C. / Bayer, P.
CitationJournal: Bmc Biol. / Year: 2016
Title: NmPin from the marine thaumarchaeote Nitrosopumilus maritimus is an active membrane associated prolyl isomerase.
Authors: Hoppstock, L. / Trusch, F. / Lederer, C. / van West, P. / Koenneke, M. / Bayer, P.
History
DepositionOct 22, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PpiC-type peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)10,1981
Polymers10,1981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein PpiC-type peptidyl-prolyl cis-trans isomerase


Mass: 10197.915 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosopumilus maritimus (archaea) / Strain: SCM1 / Gene: nmar0942, Nmar_0942 / Plasmid: pET41 (a-c) / Production host: Escherichia coli (E. coli) / References: UniProt: A9A2C7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H COSY
1512D 1H-1H NOESY
1613D CBCA(CO)NH
1713D HN(CA)CB
1823D (H)CCH-TOCSY
1923D (H)CCH-COSY
11023D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] protein, 50 mM [U-99% 13C; U-99% 15N] potassium phosphate, 2 uM [U-99% 13C; U-99% 15N] DSS, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 13C; U-99% 15N] protein, 50 mM [U-99% 13C; U-99% 15N] potassium phosphate, 2 uM [U-99% 13C; U-99% 15N] DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity-1[U-99% 13C; U-99% 15N]1
50 mMpotassium phosphate-2[U-99% 13C; U-99% 15N]1
2 uMDSS-3[U-99% 13C; U-99% 15N]1
1 mMentity-4[U-99% 13C; U-99% 15N]2
50 mMpotassium phosphate-5[U-99% 13C; U-99% 15N]2
2 uMDSS-6[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 301.5 K

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NMR measurement

NMR spectrometerType: Bruker Ultrashield / Manufacturer: Bruker / Model: Ultrashield / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3Bruker Biospincollection
TopSpin3Bruker Biospinprocessing
CCPN2.1CCPNchemical shift assignment
CCPN2.1CCPNchemical shift calculation
CCPN2.1CCPNpeak picking
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1846 / NOE intraresidue total count: 252 / NOE long range total count: 740 / NOE medium range total count: 1106 / NOE sequential total count: 436
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20
NMR ensemble rmsDistance rms dev: 1.079 Å

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