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- PDB-2bm4: The Structure of MfpA (Rv3361c, C2 Crystal form). The Pentapeptid... -

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Basic information

Entry
Database: PDB / ID: 2bm4
TitleThe Structure of MfpA (Rv3361c, C2 Crystal form). The Pentapeptide Repeat Protein from Mycobacterium tuberculosis Folds as A Right- handed Quadrilateral Beta-helix.
ComponentsPENTAPEPTIDE REPEAT FAMILY PROTEIN
KeywordsPENTAPEPTIDE REPEAT PROTEIN / PENTAPEPTIDE REPEAT PROTEINS / FLUROQUINOLONE RESISTANCE / DNA GYRASE / DNA MIMICRY / RIGHT-HANDED QUADRILATERAL BETA-HELIX
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity / response to antibiotic / protein homodimerization activity
Similarity search - Function
Pentapeptide repeats (9 copies) / Pentapeptide repeat region / : / Pentapeptide repeats (8 copies) / Pentapeptide repeat / E3 ubiquitin-protein ligase SopA / Pectate Lyase C-like / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Pentapeptide repeat family protein
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHegde, S.S. / Vetting, M.W. / Roderick, S.L. / Mitchenall, L.A. / Maxwell, A. / Takiff, H.E. / Blanchard, J.S.
CitationJournal: Science / Year: 2005
Title: A Fluroquinolone Resistance Protein from Mycobacterium Tuberculosis that Mimics DNA
Authors: Hegde, S.S. / Vetting, M.W. / Roderick, S.L. / Mitchenall, L.A. / Maxwell, A. / Takiff, H.E. / Blanchard, J.S.
History
DepositionMar 9, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PENTAPEPTIDE REPEAT FAMILY PROTEIN
B: PENTAPEPTIDE REPEAT FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)40,6522
Polymers40,6522
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)177.180, 31.109, 69.601
Angle α, β, γ (deg.)90.00, 111.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PENTAPEPTIDE REPEAT FAMILY PROTEIN / MFPA / RV3361C


Mass: 20325.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O50390
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHREE RESIDUES FROM N-TERMINAL HIS-TAG REMAIN AFTER THROMBIN CLEAVAGE OF THE TAG.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.43 %
Crystal growDetails: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 400, 100 MM AMMONIUM CITRATE PH 5.5
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 mg/mlprotein1drop
210 mMTris1drop
31 %ethylene glycol1drop
430 mMbeta-mercaptoethanol1drop
530 %PEG4001reservoir
6100 mMammonium citrate1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MSC RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 17270 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 19.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 5.8 / % possible all: 85.5
Reflection
*PLUS
Rmerge(I) obs: 0.03
Reflection shell
*PLUS
% possible obs: 85.5 % / Rmerge(I) obs: 0.13

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PREVIOUS STRUCTURE DETERMINED BY SE-MET MAD

Resolution: 2.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: MISSING RESIDUES FROM THE N AND C- TERMINI OF THE SUBMITTED COORDINATES AS COMPARED TO THE SUBMITTED SEQUENCE ARE REGIONS WHICH EXHIBITED NO ELECTRON DENSITY AND THEREFORE THEREFORE WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 834 5 %RANDOM
Rwork0.199 ---
obs0.199 17270 93.3 %-
Solvent computationSolvent model: BULK SOLVENT / Bsol: 54.7426 Å2 / ksol: 0.362602 e/Å3
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.714 Å20 Å21.92 Å2
2---4.006 Å20 Å2
3---4.719 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2761 0 0 97 2858
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.95
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree: 0.301 / Rfactor Rwork: 0.203 / Total num. of bins used: 10
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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