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- PDB-2vp8: Structure of Mycobacterium tuberculosis Rv1207 -

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Basic information

Entry
Database: PDB / ID: 2vp8
TitleStructure of Mycobacterium tuberculosis Rv1207
ComponentsDIHYDROPTEROATE SYNTHASE 2
KeywordsTRANSFERASE / DIHYDROPTEROATE SYNTHASE / MYCOBACTERIUM TUBERCULOSIS / RV1207 / FOLATE BIOSYNTHESIS / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


folic acid-containing compound biosynthetic process / dihydropteroate synthase activity / cytosol
Similarity search - Function
Dihydropteroate synthase signature 1. / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Inactive dihydropteroate synthase 2 / Inactive dihydropteroate synthase 2
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsGengenbacher, M. / Xu, T. / Niyomwattanakit, P. / Spraggon, G. / Dick, T.
Citation
Journal: Fems Microbiol.Lett. / Year: 2008
Title: Biochemical and Structural Characterization of the Putative Dihydropteroate Synthase Ortholog Rv1207 of Mycobacterium Tuberculosis.
Authors: Gengenbacher, M. / Xu, T. / Niyomwattanakit, P. / Spraggon, G. / Dick, T.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Crystal Structure of Mycobacterium Tuberculosis 6-Hydroxymethyl-7,8-Dihydropteroate Synthase in Complex with Pterin Monophosphate: New Insight Into the Enzymatic Mechanism and Sulfa-Drug Action
Authors: Baca, A.M. / Sirawaraporn, R. / Turley, S. / Sirawaraporn, W. / Hol, W.G.J.
History
DepositionFeb 27, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROPTEROATE SYNTHASE 2
B: DIHYDROPTEROATE SYNTHASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3566
Polymers66,1072
Non-polymers2484
Water99155
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-27.7 kcal/mol
Surface area24640 Å2
MethodPQS
Unit cell
Length a, b, c (Å)80.727, 80.727, 215.938
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.34353, -0.84941, 0.40061), (-0.87294, 0.1315, -0.46976), (0.34634, -0.51109, -0.78666)
Vector: -2.63996, 27.29851, 65.41853)

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Components

#1: Protein DIHYDROPTEROATE SYNTHASE 2 / DHPS 2 / DIHYDROPTEROATE PYROPHOSPHORYLASE 2 / MYCOBACTERIUM TUBERCULOSIS RV1207


Mass: 33053.656 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET-21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P64139, UniProt: P9WNC9*PLUS, EC: 2.1.5.15
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.13 Å3/Da / Density % sol: 70 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.64→107 Å / Num. obs: 24807 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.5
Reflection shellResolution: 2.64→2.8 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.6 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EYE

1eye


Resolution: 2.64→19.84 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.906 / SU B: 20.695 / SU ML: 0.212 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.37 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1231 5 %RANDOM
Rwork0.223 ---
obs0.226 23291 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å20 Å2
2--0.42 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.64→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3433 0 16 55 3504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223506
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1381.9424770
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2995461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.67422.302139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.26915513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3161535
X-RAY DIFFRACTIONr_chiral_restr0.0690.2577
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022627
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.21703
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22389
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2133
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3531.52358
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.6323678
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.84531268
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3744.51091
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: 2.64→2.71 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.346 94
Rwork0.32 1649
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)
12.77521.1493-0.81637.69753.142111.0438-0.41410.3888-0.8715-0.3280.2015-0.69221.32360.27190.21260.2041-0.16660.2023-0.0662-0.08780.1292-20.04915.9974.581
23.10514.38860.676511.30593.87248.2385-0.45740.5589-0.1702-1.06390.5682-0.6892-0.48690.7093-0.11080.1374-0.27680.07130.043-0.0022-0.0439-18.535.6040.702
35.1828-0.871-1.27016.73131.6677.0926-0.2047-0.2747-0.33730.16920.0848-0.22310.4220.17610.1199-0.1118-0.12540.0351-0.08440.0233-0.1149-20.79329.86419.905
49.736-1.7394.54273.58752.23237.2165-0.6712-1.3403-0.11030.59430.36850.00110.1138-0.60660.3028-0.06050.1173-0.00840.1114-0.0935-0.0185-6.83143.04946.732
513.8939-1.69838.03382.8947-0.42589.5828-0.4496-2.03210.24790.54050.11770.76790.0325-1.64590.33190.11730.20310.01840.4319-0.290.2997-23.94849.68545.257
619.32326.34823.31577.81968.35189.7673-0.3748-0.678-0.24670.37980.110.07820.501-0.52610.2648-0.14560.03630.0181-0.0568-0.08250.0601-26.46242.78432.674
78.686-1.07482.23014.20894.047914.6631-0.25990.16790.0916-0.25450.1554-0.1404-0.10610.50660.1046-0.2064-0.0773-0.0122-0.1198-0.0428-0.0943-13.1640.06827.21
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 142
2X-RAY DIFFRACTION2A143 - 251
3X-RAY DIFFRACTION3A267 - 311
4X-RAY DIFFRACTION4B29 - 126
5X-RAY DIFFRACTION5B127 - 224
6X-RAY DIFFRACTION6B225 - 252
7X-RAY DIFFRACTION7B266 - 310

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