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- PDB-2kvs: NMR Solution Structure of Q7A1E8 protein from Staphylococcus aure... -

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Basic information

Entry
Database: PDB / ID: 2kvs
TitleNMR Solution Structure of Q7A1E8 protein from Staphylococcus aureus: Northeast Structural Genomics Consortium target: ZR215
ComponentsUncharacterized protein MW0776
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / NESG / BIG target / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyYozE SAM-like / YozE SAM-like domain / YozE SAM-like superfamily / YozE SAM-like fold / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha / YozE SAM-like domain-containing protein / YozE_SAM_like domain-containing protein
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsSwapna, G.V.T. / Montelione, A.F. / Wang, D. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T.B. / Rost, B. / Everett, J. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR Solution Structure of Q7A1E8 protein from Staphylococcus aureus: Northeast Structural Genomics Consortium target: ZR215
Authors: Swapna, G.V.T. / Montelione, A.F. / Wang, D. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T.B. / Rost, B. / Everett, J. / Montelione, G.T.
History
DepositionMar 27, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 14, 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: database_2 / pdbx_database_status ...database_2 / 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

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Assembly

Deposited unit
A: Uncharacterized protein MW0776


Theoretical massNumber of molelcules
Total (without water)9,4531
Polymers9,4531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein MW0776


Mass: 9452.560 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MW2 / Gene: MW0776 / Production host: Escherichia coli (E. coli) / Strain (production host): XL10 / References: UniProt: Q7A1E8, UniProt: A0A0H3JVL4*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: PSI-2 BIG
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D HNCO
1713D HNHA
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11112D 1H-15N HNOE
NMR detailsText: The structure was determined using triple resonance NMR spectroscopy. Automated resonance assignments were made using AutoAssign. Sidechain assignments were completed manually. Chemical shift ...Text: The structure was determined using triple resonance NMR spectroscopy. Automated resonance assignments were made using AutoAssign. Sidechain assignments were completed manually. Chemical shift assignments were validated using AVS software. Automated NOESY assignments were made using AutoStructure and structure solution was determined using CYANA-2.1.

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Sample preparation

DetailsContents: 0.71 mM [U-100% 13C; U-100% 15N] ZR215-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.71 mM / Component: ZR215-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 100mM NaCl / pH: 7.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky2.3Goddardpeak picking
Sparky2.3Goddarddata analysis
VnmrJ2.1BVariancollection
TopSpin2.1Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.2.1Huang, Tejero, Powers and Montelionegeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AVSMoseley and Montelionechemical shift validation
PSVS1.3Bhattacharya and Montelionestructure validation
TALOSCornilescu, Delaglio and Baxdihedral angle constriants
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 400 structures were calculated and 20 best conformers were then refined in a shell of water using CNS. Initial dihedral angle constriants were obtained from TALOS. Final quality factors ...Details: 400 structures were calculated and 20 best conformers were then refined in a shell of water using CNS. Initial dihedral angle constriants were obtained from TALOS. Final quality factors determined using PSVS software. Ordered residues were defined as 8-12,18-30,35-37,43-77.RMSD(ordered residues):Backbone 1.0A, All atoms 1.5A; Ramachandran statistics for all ordered regions: Most favored regions: 91.5%; Additionally allowed: 8.4% and generously allowed: 0.1%. Procheck scores for all ordered residues are (Raw/Z): phi-psi 0.11/0.75 All:0.04/0.24; MolProbity clash score(Raw/Z):13.45/-0.78; RPF scores for goodness of fit of NOESY data: Recall: 0.954; Precision:0.928; F-measure: 0.941; DP-score 0.798.
NMR constraintsNOE constraints total: 971 / NOE intraresidue total count: 93 / NOE long range total count: 199 / NOE medium range total count: 378 / NOE sequential total count: 301
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 3.39 Å
NMR ensemble rmsDistance rms dev: 0.06 Å

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