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- PDB-5i7r: Mycobacterium tuberculosis CysM in complex with the Urea-scaffold... -

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Basic information

Entry
Database: PDB / ID: 5i7r
TitleMycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 2 [3-(3-([1,1'-biphenyl]-3-yl)ureido)benzoic acid]
ComponentsO-phosphoserine sulfhydrylase
KeywordsLYASE / Mycobacterium tuberculosis / Cysteine biosynthesis / sulphur metabolism / inhibitor
Function / homology
Function and homology information


[CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase / Cysteine synthesis from O-phosphoserine / O-phosphoserine sulfhydrylase activity / cysteine synthase activity / cysteine biosynthetic process / cysteine biosynthetic process from serine / pyridoxal phosphate binding / protein-containing complex / cytoplasm / cytosol
Similarity search - Function
Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-68W / ACETATE ION / PYRIDOXAL-5'-PHOSPHATE / O-phosphoserine sulfhydrylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsSchnell, R. / Maric, S. / Schneider, G.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: J.Med.Chem. / Year: 2016
Title: Inhibitors of the Cysteine Synthase CysM with Antibacterial Potency against Dormant Mycobacterium tuberculosis.
Authors: Brunner, K. / Maric, S. / Reshma, R.S. / Almqvist, H. / Seashore-Ludlow, B. / Gustavsson, A.L. / Poyraz, O. / Yogeeswari, P. / Lundback, T. / Vallin, M. / Sriram, D. / Schnell, R. / Schneider, G.
History
DepositionFeb 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: O-phosphoserine sulfhydrylase
A: O-phosphoserine sulfhydrylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,90211
Polymers69,4482
Non-polymers1,4549
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-15 kcal/mol
Surface area22530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.170, 86.487, 101.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein O-phosphoserine sulfhydrylase / OPS sulfhydrylase / CysO-thiocarboxylate-dependent cysteine synthase / Cysteine synthase B / CSase ...OPS sulfhydrylase / CysO-thiocarboxylate-dependent cysteine synthase / Cysteine synthase B / CSase B / O-phosphoserine-specific cysteine synthase / [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase


Mass: 34724.117 Da / Num. of mol.: 2 / Mutation: T2A, Lys51 covalent modification with PLP
Source method: isolated from a genetically manipulated source
Details: Lys51 covalent modification with PLP / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cysM, Rv1336, MTCY130.21 / Plasmid: pET28a
Details (production host): N-terminal His6-tag, Thrombin site for tag removal
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WP53, [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-68W / 3-{[([1,1'-biphenyl]-3-yl)carbamoyl]amino}benzoic acid


Mass: 332.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H16N2O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.4 Å3/Da / Density % sol: 48.8 % / Description: rod / needle
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2M NH4-acetate, 0.1M BT pH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2014 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.73→65.86 Å / Num. obs: 65578 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 19.6
Reflection shellResolution: 1.73→1.81 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3dki

3dki


Resolution: 1.73→65.85 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.597 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.104 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20671 3308 5 %RANDOM
Rwork0.17381 ---
obs0.17549 62228 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.351 Å2
Baniso -1Baniso -2Baniso -3
1-2.99 Å2-0 Å20 Å2
2---1.61 Å2-0 Å2
3----1.38 Å2
Refinement stepCycle: 1 / Resolution: 1.73→65.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4682 0 70 209 4961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194851
X-RAY DIFFRACTIONr_bond_other_d0.0010.024596
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9916604
X-RAY DIFFRACTIONr_angle_other_deg0.8733.00310513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8255621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09223.15200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70215724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1621542
X-RAY DIFFRACTIONr_chiral_restr0.0940.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215593
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021099
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_it2.3613.1422495
X-RAY DIFFRACTIONr_mcbond_other2.2873.142489
X-RAY DIFFRACTIONr_mcangle_it3.2014.6993109
X-RAY DIFFRACTIONr_mcangle_other3.2014.6993110
X-RAY DIFFRACTIONr_scbond_it3.0093.4782356
X-RAY DIFFRACTIONr_scbond_other3.0093.4792357
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.525.0873496
X-RAY DIFFRACTIONr_long_range_B_refined5.96125.7995502
X-RAY DIFFRACTIONr_long_range_B_other5.96125.8015503
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 217 -
Rwork0.292 4582 -
obs--98.58 %

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