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- PDB-2vor: Crystal Structures of Mycobacterium tuberculosis Folylpolyglutama... -

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Basic information

Entry
Database: PDB / ID: 2vor
TitleCrystal Structures of Mycobacterium tuberculosis Folylpolyglutamate Synthase Complexed with ADP and AMPPCP
ComponentsFOLYLPOLYGLUTAMATE SYNTHASE PROTEIN FOLC
KeywordsLIGASE / PEPTIDOGLYCAN SYNTHESIS / CELL DIVISION / FOLATE METABOLISM / CELL WALL BIOGENESIS/DEGRADATION
Function / homology
Function and homology information


tetrahydrofolate synthase / tetrahydrofolylpolyglutamate synthase activity / cobalt ion binding / ADP binding / magnesium ion binding / ATP binding
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 family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / 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 family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / : / tetrahydrofolate synthase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

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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)51,7538
Polymers50,8281
Non-polymers9257
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.396, 112.396, 112.396
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-1491-

CO

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Components

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


Mass: 50828.059 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
#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-CO / COBALT (II) ION


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


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


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
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: 0.97945
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 26, 2006 / Details: HORIZONTAL FOCUSING
RadiationMonochromator: SINGLE CRYSTAL SI(311) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.3→56.2 Å / Num. obs: 21320 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 42.12 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0067refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MTBFPGS ADP STRUCTURE USED AS A MODEL FOR MOLECULAR REPLACEMENT

Resolution: 2.3→79.56 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.201 / SU ML: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1091 5.1 %RANDOM
Rwork0.176 ---
obs0.178 20201 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.37 Å2
Refinement stepCycle: LAST / Resolution: 2.3→79.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3215 0 47 122 3384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223309
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0571.9784517
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6625436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32223.594128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46915480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0021525
X-RAY DIFFRACTIONr_chiral_restr0.1530.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212474
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_it0.9751.52194
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71623504
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.08531115
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7814.51013
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: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.277 94
Rwork0.218 1448
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)
10.69790.10.48293.2735-0.26791.00830.08970.2987-0.1558-0.1242-0.18440.11710.2749-0.02490.0947-0.0494-0.03280.02740.0594-0.1292-0.139312.0056-53.189419.6439
21.08380.17820.35082.5380.29131.30560.06770.02130.06070.1788-0.24680.53180.0568-0.35710.1791-0.2257-0.06650.08070.0808-0.1348-0.0946-1.6429-29.730526.3178
32.5705-0.0480.0141.8544-0.6272.39030.07390.32530.1423-0.4222-0.17360.0805-0.0957-0.11060.0997-0.09480.081-0.06810.09740.0017-0.20797.66-23.28310.4484
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 39
2X-RAY DIFFRACTION1A49 - 65
3X-RAY DIFFRACTION1A118 - 168
4X-RAY DIFFRACTION2A169 - 338
5X-RAY DIFFRACTION3A339 - 485

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