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- PDB-2kyw: Solution NMR Structure of a domain of adhesion exoprotein from Pe... -

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Basic information

Entry
Database: PDB / ID: 2kyw
TitleSolution NMR Structure of a domain of adhesion exoprotein from Pediococcus pentosaceus, Northeast Structural Genomics Consortium Target PtR41O
ComponentsAdhesion exoprotein
KeywordsCELL ADHESION / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / GFT / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


Putative peptidoglycan bound protein (lpxtg motif) / Mucin binding domain / Mub B2-like domain / Muc B2-like domain / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) ...Putative peptidoglycan bound protein (lpxtg motif) / Mucin binding domain / Mub B2-like domain / Muc B2-like domain / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesPediococcus pentosaceus (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsHe, Y. / Eletsky, A. / Mills, J.L. / Wang, H. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Lee, H.-W. ...He, Y. / Eletsky, A. / Mills, J.L. / Wang, H. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Lee, H.-W. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of a domain of adhesion exoprotein from Pediococcus pentosaceus, Northeast Structural Genomics Consortium Target PtR41O
Authors: He, Y. / Eletsky, A. / Mills, J.L. / Wang, H. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Lee, H.-W. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 9, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: pdbx_database_status / pdbx_nmr_sample_details ...pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents ..._pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 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

Downloads & links

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Assembly

Deposited unit
A: Adhesion exoprotein


Theoretical massNumber of molelcules
Total (without water)9,3091
Polymers9,3091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Adhesion exoprotein


Mass: 9308.923 Da / Num. of mol.: 1 / Fragment: sequence database residues 1287-1365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pediococcus pentosaceus (bacteria) / Strain: ATCC 25745 / Gene: PEPE_0118 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q03HU7

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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 CT-HSQC ali
1312D 1H-13C CT-HSQC aro
1413D HNCO
1513D HN(CA)CO
161GFT CBCA(CO)NH
171GFT HN(CA)CB
1813D HBHA(CO)NH
1913D (H)CCH-TOCSY
11013D (H)CCH-COSY ali
111113C/15N-NOESY
11222D 1H-13C CT-HSQC (methyl)
11322D J-modulation 1H-15N HSQC
11432D J-modulation 1H-15N HSQC
11542D J-modulation 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] PtR41O-1, 100 mM sodium chloride-2, 5 mM calcium chloride-3, 10 mM DTT-4, 20 mM MES-5, 0.02 % NaN3-6, 50 uM DSS-7, 90% H2O/10% D2O90% H2O/10% D2O
21.2 mM [U-5% 13C; U-100% 15N] PtR41O-8, 100 mM sodium chloride-9, 5 mM calcium chloride-10, 10 mM DTT-11, 20 mM MES-12, 0.02 % NaN3-13, 50 uM DSS-14, 90% H2O/10% D2O90% H2O/10% D2O
30.66 mM [U-5% 13C; U-100% 15N] PtR41O-15, 66 mM sodium chloride-16, 3.3 mM calcium chloride-17, 6.6 mM DTT-18, 13.2 mM MES-19, 0.0132 % NaN3-20, 33 uM DSS-21, 4 % poly ethylene glycol-22, 83% H2O/17% D2O83% H2O/17% D2O
40.66 mM [U-5% 13C; U-100% 15N] PtR41O-23, 66 mM sodium chloride-24, 3.3 mM calcium chloride-25, 6.6 mM DTT-26, 13.2 mM MES-27, 0.0132 % NaN3-28, 33 uM DSS-29, 13.25 mg/mL Pf1 phage-30, 83% H2O/17% D2O83% H2O/17% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMPtR41O-1[U-100% 13C; U-100% 15N]1
100 mMsodium chloride-21
5 mMcalcium chloride-31
10 mMDTT-41
20 mMMES-51
0.02 %NaN3-61
50 uMDSS-71
1.2 mMPtR41O-8[U-5% 13C; U-100% 15N]2
100 mMsodium chloride-92
5 mMcalcium chloride-102
10 mMDTT-112
20 mMMES-122
0.02 %NaN3-132
50 uMDSS-142
0.66 mMPtR41O-15[U-5% 13C; U-100% 15N]3
66 mMsodium chloride-163
3.3 mMcalcium chloride-173
6.6 mMDTT-183
13.2 mMMES-193
0.0132 %NaN3-203
33 uMDSS-213
4 %poly ethylene glycol-223
0.66 mMPtR41O-23[U-5% 13C; U-100% 15N]4
66 mMsodium chloride-244
3.3 mMcalcium chloride-254
6.6 mMDTT-264
13.2 mMMES-274
0.0132 %NaN3-284
33 uMDSS-294
13.25 mg/mLPf1 phage-304
Sample conditionsIonic strength: 117.5 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA5002
Bruker AvanceBrukerAVANCE6003
Varian INOVAVarianINOVA6004

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipe2007.030.16.06Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
TopSpinBruker Biospincollection
VnmrJ2.1BVariancollection
MOLMOLKoradi, Billeter and Wuthrichrefinement
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
CARA1.8.4Keller and Wuthrichdata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxdata analysis
PSVS1.3Bhattacharya and Montelionevalidation
NMRDraw3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
PROSAGuntertprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed iteratively with CYANA v3.0 using NOE-based constraints, PHI and PSI dihedral angle constraints from TALOS+, and RDC constraints. The 20 conformers out ...Details: Structure determination was performed iteratively with CYANA v3.0 using NOE-based constraints, PHI and PSI dihedral angle constraints from TALOS+, and RDC constraints. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field
NMR constraintsNOE constraints total: 905 / NOE intraresidue total count: 199 / NOE long range total count: 386 / NOE medium range total count: 83 / NOE sequential total count: 237
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 16

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