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- PDB-6id6: Crystal structure of Rv0731c from Mycobacterium tuberculosis at 1... -

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Basic information

Entry
Database: PDB / ID: 6id6
TitleCrystal structure of Rv0731c from Mycobacterium tuberculosis at 1.63 Angstroms.
ComponentsPutative S-adenosyl-L-methionine-dependent methyltransferase Rv0731c
KeywordsTRANSFERASE / Methyltransferase
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation
Similarity search - Function
S-adenosyl-L-methionine-dependent methyltransferase, putative / Methyltransferase Ppm1/Ppm2/Tcmp / Leucine carboxyl methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Putative S-adenosyl-L-methionine-dependent methyltransferase Rv0731c
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsBansia, H. / Kalladi, S.M. / Nagaraja, V. / Ramakumar, S.
CitationJournal: To Be Published
Title: Crystal structure of Rv0731c from Mycobacterium tuberculosis.
Authors: Bansia, H. / Kalladi, S.M. / Nagaraja, V. / Ramakumar, S.
History
DepositionSep 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr2_symmetry / _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.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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative S-adenosyl-L-methionine-dependent methyltransferase Rv0731c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2534
Polymers33,0541
Non-polymers1993
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-4 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.680, 133.680, 40.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-811-

HOH

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Components

#1: Protein Putative S-adenosyl-L-methionine-dependent methyltransferase Rv0731c


Mass: 33053.844 Da / Num. of mol.: 1 / Fragment: UNP residues 11-311
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: Rv0731c / Production host: Mycolicibacterium smegmatis (bacteria)
References: UniProt: P9WFI5, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.69 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 200mM magnesium acetate, Tris-HCL pH 8.5, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97633 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97633 Å / Relative weight: 1
ReflectionResolution: 1.63→38.47 Å / Num. obs: 44735 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.043 / Rrim(I) all: 0.124 / Net I/σ(I): 14.2 / Num. measured all: 361801 / Scaling rejects: 58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.63-1.667.11.0041561121990.6420.4021.0832.199.9
8.93-38.477.30.02922143030.9990.0110.0314199

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
Aimless0.6.3data scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→38.47 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.047 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.078
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1871 2203 4.9 %RANDOM
Rwork0.1538 ---
obs0.1554 42530 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 48.44 Å2 / Biso mean: 13.451 Å2 / Biso min: 6.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å2-0 Å2-0 Å2
2--0.24 Å2-0 Å2
3----0.48 Å2
Refinement stepCycle: final / Resolution: 1.63→38.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2302 0 12 377 2691
Biso mean--41.92 24.64 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132384
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172194
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.6413247
X-RAY DIFFRACTIONr_angle_other_deg1.5891.5785034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9445311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.04220.486144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.10815358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9741527
X-RAY DIFFRACTIONr_chiral_restr0.0950.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022779
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02562
LS refinement shellResolution: 1.63→1.672 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 162 -
Rwork0.242 3154 -
all-3316 -
obs--99.88 %
Refinement TLS params.Method: refined / Origin x: -13.0746 Å / Origin y: -39.6023 Å / Origin z: -7.8667 Å
111213212223313233
T0.0111 Å20.0109 Å20.0034 Å2-0.0143 Å20.0027 Å2--0.0072 Å2
L0.0933 °2-0.0703 °20.0666 °2-0.0576 °2-0.031 °2--0.3322 °2
S-0.0051 Å °0.0092 Å °-0.0026 Å °0.0074 Å °-0.0008 Å °0.0013 Å °-0.0287 Å °-0.0066 Å °0.0059 Å °

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