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- PDB-2vos: Mycobacterium tuberculosis Folylpolyglutamate synthase complexed ... -

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Basic information

Entry
Database: PDB / ID: 2vos
TitleMycobacterium tuberculosis Folylpolyglutamate synthase complexed with ADP
ComponentsFOLYLPOLYGLUTAMATE SYNTHASE PROTEIN FOLC
KeywordsLIGASE / PEPTIDOGLYCAN SYNTHESIS / CELL DIVISION / FOLATE METABOLISM / CELL WALL BIOGENESIS/DEGRADATION
Function / homology
Function and homology information


tetrahydrofolate synthase / dihydrofolate synthase activity / tetrahydrofolylpolyglutamate synthase activity / cobalt ion binding / ADP binding / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Folylpolyglutamate synthase signature 2. / Folylpolyglutamate synthetase / Folylpolyglutamate synthetase, conserved site / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily ...Folylpolyglutamate synthase signature 2. / Folylpolyglutamate synthetase / Folylpolyglutamate synthetase, conserved site / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Protein-Tyrosine Phosphatase; Chain A / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / tetrahydrofolate synthase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsYoung, P.G. / Baker, E.N. / Metcalf, P. / Smith, C.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structures of Mycobacterium Tuberculosisfolylpolyglutamate Synthase Complexed with Adp and Amppcp.
Authors: Young, P.G. / Smith, C.A. / Metcalf, P. / Baker, E.N.
History
DepositionFeb 19, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FOLYLPOLYGLUTAMATE SYNTHASE PROTEIN FOLC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0759
Polymers51,2031
Non-polymers8718
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.405, 112.405, 112.405
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-1492-

CO

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Components

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Protein , 1 types, 1 molecules A

#1: Protein FOLYLPOLYGLUTAMATE SYNTHASE PROTEIN FOLC / FOLYLPOLYGLUTAMATE SYNTHASE / FOLYLPOLY-GAMMA-GLUTAMATE SYNTHETASE / FPGS / FOLYLPOLYGLUTAMATE SYNTHASE


Mass: 51203.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: GST-HIS6-MTBFPGS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O53174, tetrahydrofolate synthase

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Non-polymers , 5 types, 176 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.86 % / Description: NONE
Crystal growpH: 5.5
Details: MTBFPGS PRE-INCUBATED WITH 1.5 MM ADP AND 2 MM MGCL2 WERE GROWN BY THE BATCH METHOD UNDER PARAFFIN OIL IN 2 PLUS 2 UL DROPS OF PROTEIN AND 14%(W/V) PEG 8000, 30%(V/V) MPD, 10 MM COCL2, 50 MM ...Details: MTBFPGS PRE-INCUBATED WITH 1.5 MM ADP AND 2 MM MGCL2 WERE GROWN BY THE BATCH METHOD UNDER PARAFFIN OIL IN 2 PLUS 2 UL DROPS OF PROTEIN AND 14%(W/V) PEG 8000, 30%(V/V) MPD, 10 MM COCL2, 50 MM SODIUM ACETATE PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9798
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 26, 2006 / Details: VERTICAL FOCUSING MIRROR
RadiationMonochromator: SINGLE CRYSTAL SI(311) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2→45.88 Å / Num. obs: 32271 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0067refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2→39 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.046 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1657 5.1 %RANDOM
Rwork0.157 ---
obs0.158 30585 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.37 Å2
Refinement stepCycle: LAST / Resolution: 2→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 44 168 3492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223386
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8091.9744621
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0415445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26523.603136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54615497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2211527
X-RAY DIFFRACTIONr_chiral_restr0.1320.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212550
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it11.52231
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.76223568
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.27731155
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.034.51052
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.263 133
Rwork0.19 2257
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3385-1.3672-0.16473.39550.18583.39520.0616-0.29060.33640.21530.1136-0.1289-0.10720.0615-0.1752-0.1746-0.00390.0151-0.2034-0.0779-0.130915.8639.1381.055
20.9710.0570.21390.94890.34592.10140.06090.0736-0.02760.0860.1149-0.21260.26970.3849-0.1758-0.21720.0635-0.038-0.1406-0.0719-0.090829.9991.08857.629
31.69930.01860.09231.9101-0.4281.2397-0.01570.14110.2525-0.07060.0518-0.0032-0.25490.1047-0.036-0.1709-0.04990.0268-0.21710.0303-0.091719.95727.60250.171
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 40
2X-RAY DIFFRACTION1A49 - 65
3X-RAY DIFFRACTION1A118 - 168
4X-RAY DIFFRACTION2A169 - 338
5X-RAY DIFFRACTION3A339 - 485

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