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- PDB-2ymv: Structure of Reduced M Smegmatis 5246, a homologue of M.Tuberculo... -

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Basic information

Entry
Database: PDB / ID: 2ymv
TitleStructure of Reduced M Smegmatis 5246, a homologue of M.Tuberculosis Acg
ComponentsACG NITROREDUCTASE
KeywordsOXIDOREDUCTASE / DORMANCY / REDUCED FMN
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
: / NADH Oxidase / NADH Oxidase / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / Chem-FNR / IMIDAZOLE / TRIETHYLENE GLYCOL / NAD(P)H nitroreductase acg
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChauviac, F.-X. / Bommer, M. / Dobbek, H. / Keep, N.H.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal Structure of Reduced Msacg, a Putative Nitroreductase from Mycobacterium Smegmatis and a Close Homologue of Mycobacterium Tuberculosis Acg.
Authors: Chauviac, F.-X. / Bommer, M. / Yan, J. / Parkin, G. / Daviter, T. / Lowden, P. / Raven, E.L. / Thalassinos, K. / Keep, N.H.
History
DepositionOct 10, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2May 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 / struct_conn / struct_site
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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACG NITROREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,67110
Polymers36,5871
Non-polymers1,0849
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)167.799, 167.799, 43.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-2226-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ACG NITROREDUCTASE


Mass: 36587.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2-155 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: A0R2V4

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Non-polymers , 6 types, 527 molecules

#2: Chemical ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23N4O9P
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsFMN IS THE ONLY BIOLOGICAL RELAVENT HETROGEN IN THIS ENTRY. ALL OTHER HETATOMS ARE COMPONENTS OF ...FMN IS THE ONLY BIOLOGICAL RELAVENT HETROGEN IN THIS ENTRY. ALL OTHER HETATOMS ARE COMPONENTS OF THE CRYSTALLISATION MIX AND IN THE AUTHORS' OPINION, NO BIOLOGICAL ROLE.
Sequence detailsEXTRA SER ON THE N-TERMINUS FROM TEV CLEAVAGE SITE

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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: 4.82 Å3/Da / Density % sol: 74.1 %
Description: STRUCTURE ORIGINALY SOLVED USING AUTO-RICKSHAW AND 2.4 A DATASET.
Crystal growpH: 6.5
Details: 0.1M IMIDAZOLE/MES PH 6.5, 30%(V/V)PEG550MME, 25 MM NA FORMATE, 25 MM AM ACETATE, 25 MM NA CITRATE, 25 MM NAK TARTRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9148
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 28, 2012 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9148 Å / Relative weight: 1
ReflectionResolution: 1.6→26.57 Å / Num. obs: 92796 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 15.35 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAD MODEL AT 2.4 A FROM ANOTHER DATASET

Resolution: 1.6→26.568 Å / SU ML: 0.12 / σ(F): 1.34 / Phase error: 12.95 / Stereochemistry target values: ML
Details: RESIDUES 1-2 AND 330 DISORDERED LOOP 292-294 IN MULTIPLE CONFORMATIONS
RfactorNum. reflection% reflection
Rfree0.147 4626 5 %
Rwork0.1188 --
obs0.1202 92766 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.96 Å2
Refinement stepCycle: LAST / Resolution: 1.6→26.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2533 0 73 518 3124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192759
X-RAY DIFFRACTIONf_angle_d1.7213772
X-RAY DIFFRACTIONf_dihedral_angle_d13.0351051
X-RAY DIFFRACTIONf_chiral_restr0.107430
X-RAY DIFFRACTIONf_plane_restr0.01497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.24861580.19492982X-RAY DIFFRACTION100
1.6182-1.63720.19021510.18282935X-RAY DIFFRACTION100
1.6372-1.65720.21841540.17192915X-RAY DIFFRACTION100
1.6572-1.67810.21151540.16862963X-RAY DIFFRACTION100
1.6781-1.70020.18221560.15512953X-RAY DIFFRACTION100
1.7002-1.72350.19021510.14892879X-RAY DIFFRACTION100
1.7235-1.74810.20071560.14132968X-RAY DIFFRACTION100
1.7481-1.77420.16981520.13832920X-RAY DIFFRACTION100
1.7742-1.80190.19421560.13672935X-RAY DIFFRACTION100
1.8019-1.83150.18411550.12282977X-RAY DIFFRACTION100
1.8315-1.8630.15241540.11632892X-RAY DIFFRACTION100
1.863-1.89690.15371550.10672947X-RAY DIFFRACTION100
1.8969-1.93340.14851540.1052952X-RAY DIFFRACTION100
1.9334-1.97280.12931560.10472942X-RAY DIFFRACTION100
1.9728-2.01570.14321550.10182943X-RAY DIFFRACTION100
2.0157-2.06260.12161510.10072912X-RAY DIFFRACTION100
2.0626-2.11420.13861540.09762974X-RAY DIFFRACTION99
2.1142-2.17130.13121520.09482898X-RAY DIFFRACTION99
2.1713-2.23520.1291540.08982927X-RAY DIFFRACTION100
2.2352-2.30730.11161540.08782971X-RAY DIFFRACTION100
2.3073-2.38970.12951530.08912908X-RAY DIFFRACTION99
2.3897-2.48530.13061550.09482950X-RAY DIFFRACTION99
2.4853-2.59830.12091530.09392960X-RAY DIFFRACTION99
2.5983-2.73520.13371530.1062925X-RAY DIFFRACTION99
2.7352-2.90630.13971580.11712943X-RAY DIFFRACTION99
2.9063-3.13040.14541540.12972963X-RAY DIFFRACTION99
3.1304-3.44480.15711550.13012942X-RAY DIFFRACTION99
3.4448-3.94190.13551550.12222955X-RAY DIFFRACTION98
3.9419-4.96110.12661570.11242945X-RAY DIFFRACTION98
4.9611-26.57160.17661510.16032864X-RAY DIFFRACTION93

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