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- PDB-2bm7: The Structure of MfpA (Rv3361c, P3221 Crystal form). The Pentapep... -

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Basic information

Entry
Database: PDB / ID: 2bm7
TitleThe Structure of MfpA (Rv3361c, P3221 Crystal form). The Pentapeptide Repeat Protein from Mycobacterium tuberculosis Folds as A Right- handed Quadrilateral Beta-helix.
ComponentsPENTAPEPTIDE REPEAT FAMILY PROTEIN
KeywordsPENTAPEPTIDE REPEAT PROTEIN / 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: 2.7 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
C: PENTAPEPTIDE REPEAT FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)60,9783
Polymers60,9783
Non-polymers00
Water1086
1
A: PENTAPEPTIDE REPEAT FAMILY PROTEIN
B: PENTAPEPTIDE REPEAT FAMILY PROTEIN
C: PENTAPEPTIDE REPEAT FAMILY PROTEIN

A: PENTAPEPTIDE REPEAT FAMILY PROTEIN
B: PENTAPEPTIDE REPEAT FAMILY PROTEIN
C: PENTAPEPTIDE REPEAT FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)121,9556
Polymers121,9556
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)84.080, 84.080, 147.122
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsTHE BIOLOGICALLY ACTIVE MOLECULE IS DIMERIC ANDTHE HEXAMERIC ASSEMBLY IS A TRIMER OF DIMERS. A BIOLOGICALLY ACTIVE DIMERIC ARRANGEMENT ISALSO OBSERVED IN A RELATED ENTRY 2BM4.

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Components

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


Mass: 20325.859 Da / Num. of mol.: 3
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.: 6 / 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: 2.59 Å3/Da / Density % sol: 52.18 %
Crystal growpH: 4
Details: PROTEIN (10MG/ML, 10% ETHYLENE GLYCOL, 200 MM AMMONIUM SULFATE) CRYSTALLIZED IN 30 % ETHYLENE GLYCOL, 100 MM CITRATE PHOSPHATE PH 4.0.

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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: 2.7→30 Å / Num. obs: 16076 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 46.9 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 22.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 6.3 / % possible all: 90.5

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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: 2.7→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 WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.289 784 5 %RANDOM
Rwork0.229 ---
obs0.229 16076 94 %-
Solvent computationSolvent model: SHELL MODEL / Bsol: 17.568 Å2 / ksol: 0.323291 e/Å3
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1--6.902 Å2-12.923 Å20 Å2
2---6.902 Å20 Å2
3---13.804 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4130 0 0 6 4136
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.6
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: 2.7→2.82 Å / Total num. of bins used: 10 /
Rfactor% reflection
Rfree0.323 5 %
Rwork0.276 -
obs-90.5 %

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