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- PDB-1nxj: Structure of Rv3853 from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 1nxj
TitleStructure of Rv3853 from Mycobacterium tuberculosis
ComponentsProbable S-adenosylmethionine:2-demethylmenaquinone methyltransferase
KeywordsUNKNOWN FUNCTION / beta/beta/alpha domain / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


4-hydroxy-4-methyl-2-oxoglutarate aldolase / 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity / oxaloacetate decarboxylase / ribonuclease inhibitor activity / oxaloacetate decarboxylase activity / regulation of RNA metabolic process / metal ion binding
Similarity search - Function
Regulator of ribonuclease activity A / Ribonuclease E inhibitor RraA/RraA-like / Ribonuclease E inhibitor RraA/RraA-like protein / Ribonuclease E inhibitor RraA/RraA-like superfamily / Aldolase/RraA / Glucose Oxidase; domain 1 / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLYOXYLIC ACID / L(+)-TARTARIC ACID / Putative 4-hydroxy-4-methyl-2-oxoglutarate aldolase / Putative 4-hydroxy-4-methyl-2-oxoglutarate aldolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 Å
AuthorsJohnston, J.M. / Arcus, V.L. / Baker, E.N. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Bacteriol. / Year: 2003
Title: Crystal Structure of a Putative Methyltransferase from Mycobacterium tuberculosis: Misannotation of a Genome Clarified by Protein Structural Analysis
Authors: Johnston, J.M. / Arcus, V.L. / Morton, C.J. / Parker, M.W. / Baker, E.N.
History
DepositionFeb 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable S-adenosylmethionine:2-demethylmenaquinone methyltransferase
B: Probable S-adenosylmethionine:2-demethylmenaquinone methyltransferase
C: Probable S-adenosylmethionine:2-demethylmenaquinone methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8159
Polymers58,1423
Non-polymers6726
Water4,972276
1
A: Probable S-adenosylmethionine:2-demethylmenaquinone methyltransferase
hetero molecules

A: Probable S-adenosylmethionine:2-demethylmenaquinone methyltransferase
hetero molecules

A: Probable S-adenosylmethionine:2-demethylmenaquinone methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8159
Polymers58,1423
Non-polymers6726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
2
B: Probable S-adenosylmethionine:2-demethylmenaquinone methyltransferase
hetero molecules

B: Probable S-adenosylmethionine:2-demethylmenaquinone methyltransferase
hetero molecules

B: Probable S-adenosylmethionine:2-demethylmenaquinone methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8159
Polymers58,1423
Non-polymers6726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
3
C: Probable S-adenosylmethionine:2-demethylmenaquinone methyltransferase
hetero molecules

C: Probable S-adenosylmethionine:2-demethylmenaquinone methyltransferase
hetero molecules

C: Probable S-adenosylmethionine:2-demethylmenaquinone methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8159
Polymers58,1423
Non-polymers6726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)102.462, 102.462, 117.494
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThe biological assembly is a trimer. Trimers can be generated from each of the three monomers in the assymmetric unit by the operations: -y, x-y, z; y-x, -x, z; -x, -y, z+1/2; y, y-x, z+1/2 and x-y, x, z+1/2

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Components

#1: Protein Probable S-adenosylmethionine:2-demethylmenaquinone methyltransferase


Mass: 19380.758 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MENG / Plasmid: pProEX Hta / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pRI592
References: UniProt: P0A666, UniProt: P9WGY3*PLUS, EC: 2.1.-.-
#2: Chemical ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE / GLYOXYLATE


Mass: 74.035 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H2O3
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 3.43 Å3/Da / Density % sol: 63.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.45M sodium potassium tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal
*PLUS
Density % sol: 63.9 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMTris-HCl1drop
2140 mM1droppH8.0NaCl
32 mg/mlprotein1drop
40.45 Mpotassium/sodium tartrate tetrahydrate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8452 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 20, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8452 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. all: 54630 / Num. obs: 54241 / % possible obs: 99.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 9.4 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.4
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 3.1 / Num. unique all: 5249 / % possible all: 96.1
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 54630 / Redundancy: 3.35 %
Reflection shell
*PLUS
% possible obs: 96.1 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→24.61 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 5344 10.1 %RANDOM
Rwork0.19 ---
all-55019 --
obs-52727 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.1134 Å2 / ksol: 0.395904 e/Å3
Displacement parametersBiso mean: 15.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å2-0.39 Å20 Å2
2--0.66 Å20 Å2
3----1.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.9→24.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 45 276 3705
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.011.5
X-RAY DIFFRACTIONc_mcangle_it1.412
X-RAY DIFFRACTIONc_scbond_it1.752
X-RAY DIFFRACTIONc_scangle_it2.392.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.252 488 10.3 %
Rwork0.225 4266 -
obs-4754 87.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP+LIGANDS4.PARAMPROTEIN+LIGANDS4.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CNSGLYOXALATE.PARCNSGLYOXALATE.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7
LS refinement shell
*PLUS
Num. reflection Rwork: 5344

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