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- PDB-2bm6: The Structure of MfpA (Rv3361c, C2221 Crystal form). The Pentapep... -

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Basic information

Entry
Database: PDB / ID: 2bm6
TitleThe Structure of MfpA (Rv3361c, C2221 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 (8 copies) / E3 ubiquitin-protein ligase SopA / Pentapeptide repeats (9 copies) / Pentapeptide repeat / 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 / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PENTAPEPTIDE REPEAT FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1237
Polymers20,3261
Non-polymers7976
Water1,35175
1
A: PENTAPEPTIDE REPEAT FAMILY PROTEIN
hetero molecules

A: PENTAPEPTIDE REPEAT FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,24714
Polymers40,6522
Non-polymers1,59512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)33.393, 48.573, 188.367
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2015-

HOH

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Components

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


Mass: 20325.859 Da / Num. of mol.: 1
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: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cs
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1.88 Å3/Da / Density % sol: 34.02 %
Crystal growpH: 5.5
Details: PROTEIN (10 MG/ML, 10 MM AMMONIUM CITRATE PH 7.5, 30 MM BETA-MERCAPTOETHANOL) CRYSTALLIZED IN 35% 2-ETHOXYETHANOL, 100 MM CITRATE PH 5.5. CRYSTAL WAS SOAKED IN 100 MM MES PH 5.2, 30 % ...Details: PROTEIN (10 MG/ML, 10 MM AMMONIUM CITRATE PH 7.5, 30 MM BETA-MERCAPTOETHANOL) CRYSTALLIZED IN 35% 2-ETHOXYETHANOL, 100 MM CITRATE PH 5.5. CRYSTAL WAS SOAKED IN 100 MM MES PH 5.2, 30 % PEG400, 1 M CESIUM CHLORIDE PRIOR TO VITRIFICATION AND DATA COLLECTION.

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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: 8004 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 8 / % possible all: 92.3

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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 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
Rfree0.256 424 5 %RANDOM
Rwork0.197 ---
obs0.197 7575 97.1 %-
Solvent computationSolvent model: SHELL MODEL / Bsol: 42.6576 Å2 / ksol: 0.325602 e/Å3
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.052 Å20 Å20 Å2
2---4.034 Å20 Å2
3---0.982 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1371 0 6 75 1452
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_deg1.92
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 / Total num. of bins used: 10 /
Rfactor% reflection
Rfree0.276 5 %
Rwork0.212 -

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