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- PDB-2kd7: Solution NMR structure of F5/8 type C-terminal domain of a putati... -

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Basic information

Entry
Database: PDB / ID: 2kd7
TitleSolution NMR structure of F5/8 type C-terminal domain of a putative chitobiase from Bacteroides thetaiotaomicron. Northeast Structural Genomics Consortium target BtR324B
ComponentsPutative chitobiase
KeywordsCELL ADHESION / F5/8 type C-domain / beta-sandwich / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Domain of unknown function DUF1735 / BT_3987-like, N-terminal domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsEletsky, A. / Mills, J.L. / Lee, H. / Lee, D. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G.V.T. ...Eletsky, A. / Mills, J.L. / Lee, H. / Lee, D. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Prestegard, J.H. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of F5/8 type C-terminal domain of a putative chitobiase from Bacteroides thetaiotaomicron.
Authors: Eletsky, A. / Mills, J.L. / Lee, H. / Lee, D. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Prestegard, J.H. / Szyperski, T.
History
DepositionJan 4, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative chitobiase


Theoretical massNumber of molelcules
Total (without water)17,5511
Polymers17,5511
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative chitobiase


Mass: 17550.561 Da / Num. of mol.: 1 / Fragment: UNP residues 291-440 / Mutation: K4T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Strain: DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_0865 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8A9F0

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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 ali
1312D 1H-13C CT-HSQC ali
1412D 1H-13C CT-HSQC aro
1511D 1H-15N HSQC T1
1611D 1H-15N HSQC T2
1713D HNCO
1813D CBCA(CO)NH
1913D HN(CA)CB
11013D HBHA(CO)NH
11113D HN(CA)CO
11213D (H)CCH-COSY ali
11313D (H)CCH-TOCSY ali
11413D (H)CCH-COSY aro
11513D (H)CCH-TOCSY aro
11612D 1H-15N LR-HSQC
11712D 1H-15N MEXICO
11813D 1H-15N/13Cali/13Caro NOESY
11913D 1H-13Cali NOESY
12022D 1H-13C CT-HSQC methyl LV
12122D 1H-15N HSQC
12222D 1H-13C TROSY
12332D 1H-15N HSQC
12432D 1H-15N TROSY
12542D 1H-15N HSQC
12642D 1H-15N TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-100% 13C; U-100% 15N] BtR324B-1, 20 mM ammonium acetate-2, 200 mM sodium chloride-3, 5 mM calcium chloride-4, 10 mM DTT-5, 0.02 mM sodium azide-6, 95% H2O/5% D2O95% H2O/5% D2O
21.1 mM [U-5% 13C; U-100% 15N] BtR324B-7, 20 mM ammonium acetate-8, 200 mM sodium chloride-9, 5 mM calcium chloride-10, 10 mM DTT-11, 0.02 mM sodium azide-12, 95% H2O/5% D2O95% H2O/5% D2O
31.1 mM [U-5% 13C; U-100% 15N] BtR324B-13, 20 mM ammonium acetate-14, 200 mM sodium chloride-15, 5 mM calcium chloride-16, 10 mM DTT-17, 0.02 mM sodium azide-18, 7% polyacrylamide gel-19, 88% H2O/12% D2O88% H2O/12% D2O
40.76 mM [U-5% 13C; U-100% 15N] BtR324B-20, 20 mM ammonium acetate-21, 200 mM sodium chloride-22, 5 mM calcium chloride-23, 10 mM DTT-24, 0.02 mM sodium azide-25, 4.2% polyethylene glycol-26, 1.5% hexanol-27, 88% H2O/12% D2O88% H2O/12% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMBtR324B-1[U-100% 13C; U-100% 15N]1
20 mMammonium acetate-21
200 mMsodium chloride-31
5 mMcalcium chloride-41
10 mMDTT-51
0.02 mMsodium azide-61
1.1 mMBtR324B-7[U-5% 13C; U-100% 15N]2
20 mMammonium acetate-82
200 mMsodium chloride-92
5 mMcalcium chloride-102
10 mMDTT-112
0.02 mMsodium azide-122
1.1 mMBtR324B-13[U-5% 13C; U-100% 15N]3
20 mMammonium acetate-143
200 mMsodium chloride-153
5 mMcalcium chloride-163
10 mMDTT-173
0.02 mMsodium azide-183
7 %polyacrylamide gel-193
0.76 mMBtR324B-20[U-5% 13C; U-100% 15N]4
20 mMammonium acetate-214
200 mMsodium chloride-224
5 mMcalcium chloride-234
10 mMDTT-244
0.02 mMsodium azide-254
4.2 %polyethylene glycol-264
1.5 %hexanol-274
Sample conditionsIonic strength: 215 / pH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.1BVariancollection
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
PROSA6.0.2Guntertprocessing
CARA1.8.4.2Keller and Wuthrichdata analysis
CARA1.8.4.2Keller and Wuthrichchemical shift assignment
CARA1.8.4.2Keller and Wuthrichpeak picking
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
TALOS2007.068.09.07Cornilescu, Delaglio and Baxdata analysis
CNS1.2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
PSVS1.3Bhattacharya and Montelionestructure validation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed iteratively with CYANA v2.1 and CYANA v3.0 using NOE-based constraints, PHI and PSI dihedral angle constraints from TALOS, hydrogen bond constraints ...Details: Structure determination was performed iteratively with CYANA v2.1 and CYANA v3.0 using NOE-based constraints, PHI and PSI dihedral angle constraints from TALOS, hydrogen bond constraints based on preliminary structures and MEXICO data, and RDCs from two alignment media. 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: 4123 / NOE intraresidue total count: 745 / NOE long range total count: 1951 / NOE medium range total count: 524 / NOE sequential total count: 903 / Hydrogen bond constraints total count: 212 / Protein phi angle constraints total count: 64 / Protein psi angle constraints total count: 64
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: 0.328 Å
NMR ensemble rmsDistance rms dev: 0.01 Å

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