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- PDB-2k3a: NMR solution structure of Staphylococcus saprophyticus CHAP (cyst... -

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Basic information

Entry
Database: PDB / ID: 2k3a
TitleNMR solution structure of Staphylococcus saprophyticus CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain protein. Northeast Structural Genomics Consortium target SyR11
ComponentsCHAP domain protein
KeywordsHYDROLASE / Protein / monomer / CHAP domain / putative amidase / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / HYDROLASE ANTIGEN
Function / homologyCHAP domain profile. / CHAP domain / CHAP domain / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta / Putative secretory antigen
Function and homology information
Biological speciesStaphylococcus saprophyticus subsp. saprophyticus ATCC 15305 (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailsCHAP domain, putative amidase
AuthorsRossi, P. / Aramini, J.M. / Chen, C.X. / Nwosu, C. / Cunningham, K.C. / Owens, L.A. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. ...Rossi, P. / Aramini, J.M. / Chen, C.X. / Nwosu, C. / Cunningham, K.C. / Owens, L.A. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2008
Title: Structural elucidation of the Cys-His-Glu-Asn proteolytic relay in the secreted CHAP domain enzyme from the human pathogen Staphylococcus saprophyticus.
Authors: Rossi, P. / Aramini, J.M. / Xiao, R. / Chen, C.X. / Nwosu, C. / Owens, L.A. / Maglaqui, M. / Nair, R. / Fischer, M. / Acton, T.B. / Honig, B. / Rost, B. / Montelione, G.T.
History
DepositionApr 29, 2008Deposition site: BMRB / Processing site: RCSB
SupersessionMay 13, 2008ID: 2JRN
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHAP domain protein


Theoretical massNumber of molelcules
Total (without water)15,9231
Polymers15,9231
Non-polymers00
Water0
1


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

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Components

#1: Protein CHAP domain protein /


Mass: 15922.929 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 (bacteria)
Species: Staphylococcus saprophyticus / Strain: ATCC 15305 / DSM 20229 / Description: SyR11-21.5 / Gene: SSP0609 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q49ZM2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Secretory Antigen Cysteine Peptidase
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-15N NOESY
1413D 1H-13C NOESY
1513D HN(CA)CB
1613D HNCA
1713D HNCO
1813D HBHA(CO)NH
1913D (H)CCH-TOCSY
11013D (H)CCH-COSY
11113D CCH-TOCSY
11213D HN(COCA)CB
11313D HN(CA)CO
11422D 1H-13C HSQC
1152T1/T2 relaxation
1162N15 Het-NOE

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Sample preparation

Details
Solution-IDContentsSolvent system
10.66 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM Calcium Chloride, 5 % D2O, 95% H2O/5% D2O95% H2O/5% D2O
20.96 mM [5% 13C; U-100% 15N] protein, 20 mM MES, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM Calcium Chloride, 5 % D2O, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.66 mMentity[U-100% 13C; U-100% 15N]1
20 mMMES1
100 mMDTT1
100 mMsodium chloride1
0.02 %sodium azide1
5 mMCalcium Chloride1
5 %D2O1
0.96 mMentity[5% 13C; U-100% 15N]2
20 mMMES2
100 mMDTT2
100 mMsodium chloride2
0.02 %sodium azide2
5 mMCalcium Chloride2
5 %D2O2
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospindata acquisition
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.113Goddarddata analysis
AutoAssign2Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoStructure2.1.1Huang, Tejero, Powers and Montelionestructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.11.2Schwieters, Kuszewski, Tjandra and Clorerefinement
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
MOLMOL2k2Koradi, Billeter and Wuthrichvisualization
PSVS1.3Bhattacharya and Montelionevalidation
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thovalidation
PROSASipplvalidation
PdbStatTejero R.; Montelione GTvalidation
MolProbityRichardsonvalidation
VERIFY3DLuethy et. al.validation
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS MADE WITH ITERATIVE METHOD USING CYANA-2.1 FOR SIMULATED ANNEALING AND AUTOSTRUCTURE 2.1. LOWEST TARGET FUNCTION ...Details: STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS MADE WITH ITERATIVE METHOD USING CYANA-2.1 FOR SIMULATED ANNEALING AND AUTOSTRUCTURE 2.1. LOWEST TARGET FUNCTION SELECTED. CONVERGED STRUCTURES ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NIELGES PROTOCOL WITH PARAM19). MONOMER UNDER NMR CONDITIONS. TC = 7.0 +/- 0.1 NS (1D T1/T2). ASSIGNMENT STATS (EXCLUDING C-TERM TAG): BACKBONE 98.1%, SIDECHAIN 92.0%, AROMATIC (SC) 92.45%, VL METHYL STEREOSPECIFIC 88.23%, UNAMBIGUOS SIDECHAIN NH2 100%. STRUCTURE BASED ON 1111 NOE, 70 H-BOND, 124 DIHEDRAL. 100 STRUCTURES CALCULATED 20 LOWEST ENERGY SUBMITTED. MAX NOE VIOLATION 0.34 A (1MODEL), MAX DIHEDRAL 3.60 DEG. STRUCTURE QUALITY FACTOR PSVS 1.3: ORDERED RESIDUES RANGES - ALPHA HELIX (57-64, 76-86, 143-146), B-STRAND (89-91, 150-153, 98-101, 110-116, 122-127, 136-141) [S(PHI)+S(PSI)] > 1.8. RMSD 0.5 BB, 0.8 ALL HEAVY ATOMS. RAMA: 92.4% MOST FAV, 7.6% ADDTL. ALL., 0.0 GEN. ALL., 0.0% DISALL. PROCHECK (PSI-PHI): -0.30/-0.87 (RAW/Z), PROCHECK (ALL): -0.20/-1.18 (RAW/Z), MOLPROBITY CLASH: 11.42/-0.43 (RAW/Z) . RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.925, PRECISION: 0.884, F-MEASURE: 0.904, DP-SCORE: 0.763.
NMR constraintsNOE constraints total: 1837 / NOE intraresidue total count: 402 / NOE long range total count: 687 / NOE medium range total count: 233 / NOE sequential total count: 515
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.19 Å
NMR ensemble rmsDistance rms dev: 0.01 Å

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