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- PDB-2n7j: Sidechain chi1 distribution in B3 domain of protein G from extens... -

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Basic information

Entry
Database: PDB / ID: 2n7j
TitleSidechain chi1 distribution in B3 domain of protein G from extensive sets of residual dipolar couplings
ComponentsImmunoglobulin G-binding protein G
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Ubiquitin-like (UB roll) - #10 / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Ubiquitin-like (UB roll) - #10 / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive 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
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. 'group G' (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsGrishaev, A. / Li, F. / Ying, J. / Bax, A.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Side Chain Conformational Distributions of a Small Protein Derived from Model-Free Analysis of a Large Set of Residual Dipolar Couplings.
Authors: Li, F. / Grishaev, A. / Ying, J. / Bax, A.
History
DepositionSep 12, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,2151
Polymers6,2151
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 / 100structures with favorable non-bond energy
RepresentativeModel #1sidechain conformers in their most populated conformations

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Components

#1: Antibody Immunoglobulin G-binding protein G / IgG-binding protein G


Mass: 6214.848 Da / Num. of mol.: 1 / Fragment: residues 299-352
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria) / Gene: spg / Production host: Escherichia coli (E. coli) / Variant (production host): BL21-DE3 / References: UniProt: P06654

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The backbone structure of the B3 domain of protein G is obtained as a single-conformation fit of an extensive set of backbone and Ca-Cb RDCs measured under multiple alignment orientations. ...Details: The backbone structure of the B3 domain of protein G is obtained as a single-conformation fit of an extensive set of backbone and Ca-Cb RDCs measured under multiple alignment orientations. Sidechain chi1 angle distributions are obtained from an ensemble fit to the experimental sidechain RDCs measured under six alignment orientations. Fitted data included separate CB-HB2 and CB-HB3 RDCs when available, as well as their sums (measured separately) as well as Cb-Cg RDCs where available.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111ARTSY
124ARTSY
135ARTSY
148ARTSY
159ARTSY
1612ARTSY
1713ARTSY
1816ARTSY
191CT-HN(COCA)CB
1105CT-HN(COCA)CB
1119CT-HN(COCA)CB
11213CT-HN(COCA)CB
11321H-13C HSQC
11461H-13C HSQC
115101H-13C HSQC
116141H-13C HSQC
11721H-13C CT-HSQC
11861H-13C CT-HSQC
119101H-13C CT-HSQC
120141H-13C CT-HSQC
1213DEPT-filtered 1H-13C CT-HSQC
1227DEPT-filtered 1H-13C CT-HSQC
12311DEPT-filtered 1H-13C CT-HSQC
12415DEPT-filtered 1H-13C CT-HSQC
1254HN(CO)CA
1268HN(CO)CA
12712HN(CO)CA
12816HN(CO)CA
NMR detailsText: MODEL 1 SHOWS THE SIDECHAIN CONFORMERS IN THEIR MOST POPULATED CONFORMATIONS. MODELS 2-20 SHOW THE STATISTICAL DISTRIBUTION OF SIDECHAIN CONFORMERS CONSISTENT WITH THE SIDECHAIN RDC DATA. NOTE ...Text: MODEL 1 SHOWS THE SIDECHAIN CONFORMERS IN THEIR MOST POPULATED CONFORMATIONS. MODELS 2-20 SHOW THE STATISTICAL DISTRIBUTION OF SIDECHAIN CONFORMERS CONSISTENT WITH THE SIDECHAIN RDC DATA. NOTE THAT EXCEPT FOR RESIDUES POPULATING A SINGLE NARROWLY DISTRIBUTED RANGE OF CHI1 VALUES, SIDECHAIN RDCS ARE INCONSISTENT WITH ANY OF THE INDIVIDUAL MODELS.

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Sample preparation

Details
Solution-IDContentsSolvent system
12.5 mM [U-100% 13C; U-100% 15N] wild-type GB3, 95% H2O/5% D2O95% H2O/5% D2O
22.5 mM [U-100% 13C; U-100% 15N] wild-type GB3, 100% D2O100% D2O
32.5 mM [U-100% 13C; U-100% 15N; U-75% 2H] GB3-K19A/V42E/D47K, 100% D2O100% D2O
42.5 mM [U-13C; U-15N; U-2H] wild-type GB3, 95% H2O/5% D2O95% H2O/5% D2O
50.9 mM [U-13C; U-15N] GB3-K4A/K19E/V42E-CHis6, 95% H2O/5% D2O95% H2O/5% D2O
60.9 mM [U-13C; U-15N] GB3-K4A/K19E/V42E-CHis6, 100% D2O100% D2O
70.9 mM [U-100% 13C; U-100% 15N; U-75% 2H] GB3-K4A/K19E/V42E-CHis6, 100% D2O100% D2O
80.9 mM [U-13C; U-15N; U-2H] GB3-K4A/K19E/V42E-CHis6, 95% H2O/5% D2O95% H2O/5% D2O
91.3 mM [U-13C; U-15N] GB3-K19A/V42E/D47K, 95% H2O/5% D2O95% H2O/5% D2O
101.3 mM [U-13C; U-15N] GB3-K19A/V42E/D47K, 100% D2O100% D2O
111.3 mM [U-100% 13C; U-100% 15N; U-75% 2H] GB3-K19A/V42E/D47K, 100% D2O100% D2O
121.3 mM [U-13C; U-15N; U-2H] GB3-K19A/V42E/D47K, 95% H2O/5% D2O95% H2O/5% D2O
132.0 mM [U-100% 13C; U-100% 15N] GB3-K4A/K19E/V42E, 95% H2O/5% D2O95% H2O/5% D2O
142.0 mM [U-100% 13C; U-100% 15N] GB3-K4A/K19E/V42E, 100% D2O100% D2O
152.0 mM [U-100% 13C; U-100% 15N; U-75% 2H] GB3-K4A/K19E/V42E, 100% D2O100% D2O
162.0 mM [U-13C; U-15N; U-2H] GB3-K4A/K19E/V42E, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.5 mMwild-type GB3-1[U-100% 13C; U-100% 15N]1
2.5 mMwild-type GB3-2[U-100% 13C; U-100% 15N]2
2.5 mMGB3-K19A/V42E/D47K-3[U-100% 13C; U-100% 15N; U-75% 2H]3
2.5 mMwild-type GB3-4[U-13C; U-15N; U-2H]4
0.9 mMGB3-K4A/K19E/V42E-CHis6-5[U-13C; U-15N]5
0.9 mMGB3-K4A/K19E/V42E-CHis6-6[U-13C; U-15N]6
0.9 mMGB3-K4A/K19E/V42E-CHis6-7[U-100% 13C; U-100% 15N; U-75% 2H]7
0.9 mMGB3-K4A/K19E/V42E-CHis6-8[U-13C; U-15N; U-2H]8
1.3 mMGB3-K19A/V42E/D47K-9[U-13C; U-15N]9
1.3 mMGB3-K19A/V42E/D47K-10[U-13C; U-15N]10
1.3 mMGB3-K19A/V42E/D47K-11[U-100% 13C; U-100% 15N; U-75% 2H]11
1.3 mMGB3-K19A/V42E/D47K-12[U-13C; U-15N; U-2H]12
2.0 mMGB3-K4A/K19E/V42E-13[U-100% 13C; U-100% 15N]13
2.0 mMGB3-K4A/K19E/V42E-14[U-100% 13C; U-100% 15N]14
2.0 mMGB3-K4A/K19E/V42E-15[U-100% 13C; U-100% 15N; U-75% 2H]15
2.0 mMGB3-K4A/K19E/V42E-16[U-13C; U-15N; U-2H]16
Sample conditionsIonic strength: 0.05 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Avance IIIBrukerAvance III6001
Bruker Avance IIIBrukerAvance III9002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SPARKYGoddarddata analysis
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STRUCTURES WERE OBTAINED BY A SINGLE-CONFORMER SIMULATED ANNEALING REFINEMENT WITH VARIABLE ALIGNMENT TENSORS AGAINST AN EXTENSIVE SET OF BACKBONE AND CA-CB RDCS IN MULTIPLE ALIGNMENT MEDIA, ...Details: STRUCTURES WERE OBTAINED BY A SINGLE-CONFORMER SIMULATED ANNEALING REFINEMENT WITH VARIABLE ALIGNMENT TENSORS AGAINST AN EXTENSIVE SET OF BACKBONE AND CA-CB RDCS IN MULTIPLE ALIGNMENT MEDIA, J-COUPLINGS INCLUDING HN-HA, C'-C', AND THROUGH HYDROGEN BOND N-C', AND A BACKBONE-BACKBONE HYDROGEN BONDING DATABASE-DERIVED POTENTIAL OF MEAN FORCE. BACKBONE GEOMETRIES RESULTING FROM THIS STEP WERE KEPT FIXED UP TO CB ATOMS AND CHI1 TORSION ANGLES WERE RANDOMLY SELECTED TO SAMPLE THE DISTRIBUTIONS DERIVED FROM THE ANALYSIS OF AN EXTENSIVE DATASET OF CB-CG AND CB-HB RDCS IN 6 ALIGNMENT MEDIA. CLASHING WAS MINIMIZED BY RANDOMLY SAMPLING CHI2, CHI3 AND CHI4 TORSION ANGLES SELECTED FROM THE KINEMAGE DATABASE. MODELS 2-20 SHOWING MINIMAL CLASHING WERE THEN SELECTED FOR DEPOSITION.
NMR constraintsHydrogen bond constraints total count: 34
NMR representativeSelection criteria: sidechain conformers in their most populated conformations
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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