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- PDB-5i6d: Mycobacterium tuberculosis CysM in complex with the Urea-scaffold... -

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Basic information

Entry
Database: PDB / ID: 5i6d
TitleMycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 5 [3-(3-(p-Tolyl)ureido) benzoic acid]
ComponentsO-phosphoserine sulfhydrylase
KeywordsLYASE / Cysteine synthase / Mycobacterium tuberculosis / inhibitor / transferase
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
3-{[(4-methylphenyl)carbamoyl]amino}benzoic acid / PYRIDOXAL-5'-PHOSPHATE / O-phosphoserine sulfhydrylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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 16, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 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
A: O-phosphoserine sulfhydrylase
B: O-phosphoserine sulfhydrylase
C: O-phosphoserine sulfhydrylase
D: O-phosphoserine sulfhydrylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,15014
Polymers138,8964
Non-polymers2,25410
Water16,069892
1
A: O-phosphoserine sulfhydrylase
B: O-phosphoserine sulfhydrylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6678
Polymers69,4482
Non-polymers1,2196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-16 kcal/mol
Surface area20720 Å2
MethodPISA
2
C: O-phosphoserine sulfhydrylase
D: O-phosphoserine sulfhydrylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4836
Polymers69,4482
Non-polymers1,0354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-18 kcal/mol
Surface area22130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.552, 76.373, 80.865
Angle α, β, γ (deg.)94.57, 108.24, 107.65
Int Tables number1
Space group name H-MP1

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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.: 4 / Mutation: T2A, K51:PLP-bound Lysine
Source method: isolated from a genetically manipulated source
Details: CysM, OPS dependent cysteine synthase, covalently bound PLP cofactor at Lys51
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cysM, Rv1336, MTCY130.21 / Plasmid: pET28a / 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.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-AU6 / 3-{[(4-methylphenyl)carbamoyl]amino}benzoic acid


Mass: 270.283 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H14N2O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 892 / 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: 2.57 Å3/Da / Density % sol: 52.3 % / Description: needle / rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2M MgCl2, 0.1M MES pH 6, PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91843 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2014
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91843 Å / Relative weight: 1
ReflectionResolution: 1.64→47.7 Å / Num. obs: 163557 / % possible obs: 96.9 % / Observed criterion σ(I): 1.8 / Redundancy: 2.4 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 12.9
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 1.8 / % possible all: 90.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimless0.2.8data scaling
MOLREP11.2.05phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DKI

3dki


Resolution: 1.64→47.47 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.904 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.079 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18606 8180 5 %RANDOM
Rwork0.16343 ---
obs0.16457 155374 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.632 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å20.06 Å2-0.32 Å2
2--0.88 Å2-0.85 Å2
3---0.96 Å2
Refinement stepCycle: 1 / Resolution: 1.64→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8922 0 92 892 9906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0199222
X-RAY DIFFRACTIONr_bond_other_d0.0010.028807
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.98812557
X-RAY DIFFRACTIONr_angle_other_deg0.8553.00220144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55551175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.2722.812377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.354151394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.191584
X-RAY DIFFRACTIONr_chiral_restr0.0910.21416
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110536
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022086
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_it1.7642.4214724
X-RAY DIFFRACTIONr_mcbond_other1.7642.4214723
X-RAY DIFFRACTIONr_mcangle_it2.6673.625891
X-RAY DIFFRACTIONr_mcangle_other2.6663.625892
X-RAY DIFFRACTIONr_scbond_it2.4042.7424498
X-RAY DIFFRACTIONr_scbond_other2.4032.7424498
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.763.9976667
X-RAY DIFFRACTIONr_long_range_B_refined5.92821.08111110
X-RAY DIFFRACTIONr_long_range_B_other5.92821.08411111
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.64→1.681 Å
RfactorNum. reflection% reflection
Rfree0.285 543 5 %
Rwork0.271 10978 -
obs--92.47 %

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