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- PDB-2m30: Solution NMR refinement of a metal ion bound protein using quantu... -

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Basic information

Entry
Database: PDB / ID: 2m30
TitleSolution NMR refinement of a metal ion bound protein using quantum mechanical/molecular mechanical and molecular dynamics methods
ComponentsRepressor protein
KeywordsTRANSCRIPTION REPRESSOR / metal ion refinement
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / identical protein binding / metal ion binding
Similarity search - Function
Bacterial regulatory protein, arsR family / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ArsR family transcriptional regulator / Repressor protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / molecular dynamics, quantum mechanical molecular mechanical molecular dynamics
Model detailsfewest violations, model 1
AuthorsChakravorty, D.K. / Wang, B.I. / Lee, C.I. / Guerra, A.J. / Giedroc, D.P. / Merz Jr., K.M. / Arunkumar, A.I. / Pennella, M. / Kong, X.
CitationJournal: J.Biomol.Nmr / Year: 2013
Title: Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods.
Authors: Chakravorty, D.K. / Wang, B. / Lee, C.W. / Guerra, A.J. / Giedroc, D.P. / Merz, K.M.
History
DepositionJan 4, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Repressor protein
B: Repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1464
Polymers24,0152
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3229 Å2
ΔGint-95.8 kcal/mol
Surface area11085 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 132000Structures from 1 ns of independent QM/MM MD sampling
RepresentativeModel #1fewest violations

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Components

#1: Protein Repressor protein /


Mass: 12007.708 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: czrA / Production host: Escherichia coli (E. coli) / References: UniProt: Q7A4C3, UniProt: O85142*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Refinement of the metal ion coordination in zinc-bound CzrA
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N TROSY
1212D 1H-13C HMQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D C(CO)NH
1613D H(CCO)NH
1713D HNCO
1812D 1H-15N IPAP-HSQC
1913D 1H-15N NOESY-TROSY
NMR detailsText: Residual Dipolar Couplings were measured in anisotropic environment using phage or gels.

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM [U-100% 13C; U-100% 15N] CzrA, 2.4 mM Zinc ion, 10 mM [U-100% 2H] MES, 50 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
22 mM [U-2H; U-15N]; [U-13C]-Ile,Leu,Val-methyl CzrA, 2.4 mM Zinc ion, 10 mM [U-100% 2H] MES, 50 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMCzrA-1[U-100% 13C; U-100% 15N]1
2.4 mMZinc ion-21
10 mMMES-3[U-100% 2H]1
50 mMsodium chloride-41
2 mMCzrA-5[U-2H; U-15N]; [U-13C]-Ile,Leu,Val-methyl2
2.4 mMZinc ion-62
10 mMMES-7[U-100% 2H]2
50 mMsodium chloride-82
Sample conditionsIonic strength: 50 / pH: 6.0 / Pressure: 1 atm / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA9003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SPARKYGoddardpeak picking
SPARKYGoddardchemical shift assignment
SPARKYGoddarddata analysis
MARS(MARS)-Jung and Zweckstetterchemical shift assignment
AMBER11David Case et al.structure solution
AMBER11David Case et al.refinement
AMBER11David Case et al.geometry optimization
AMBER11David Case et al.data analysis
RefinementMethod: molecular dynamics, quantum mechanical molecular mechanical molecular dynamics
Software ordinal: 1
Details: 132 ns of combined NOE and RDC constrained molecular dynamics and quantum mechanical / molecular mechanical molecular dynamics
NMR constraintsNOE constraints total: 756 / NOE intraresidue total count: 24 / NOE long range total count: 188 / NOE medium range total count: 292 / NOE sequential total count: 252
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: Structures from 1 ns of independent QM/MM MD sampling
Conformers calculated total number: 132000 / Conformers submitted total number: 10

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