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- PDB-5i7h: Mycobacterium tuberculosis CysM in complex with the Urea-scaffold... -

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Basic information

Entry
Database: PDB / ID: 5i7h
TitleMycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 6 [3-(3-(4-Bromophenyl)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 biosynthetic process / cysteine synthase activity / cysteine biosynthetic process from serine / pyridoxal phosphate binding / protein-containing complex / cytosol / cytoplasm
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-bromophenyl)carbamoyl]amino}benzoic acid / PYRIDOXAL-5'-PHOSPHATE / O-phosphoserine sulfhydrylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 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 17, 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
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)141,26113
Polymers138,8964
Non-polymers2,3659
Water4,738263
1
A: O-phosphoserine sulfhydrylase
B: O-phosphoserine sulfhydrylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6136
Polymers69,4482
Non-polymers1,1654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-15 kcal/mol
Surface area21040 Å2
MethodPISA
2
C: O-phosphoserine sulfhydrylase
D: O-phosphoserine sulfhydrylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6487
Polymers69,4482
Non-polymers1,2005
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-25 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.591, 76.089, 80.716
Angle α, β, γ (deg.)94.33, 108.32, 107.66
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, 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) / Strain: ATCC 25618 / H37Rv / 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-68V / 3-{[(4-bromophenyl)carbamoyl]amino}benzoic acid


Mass: 335.153 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H11BrN2O3
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.52 Å3/Da / Density % sol: 51.2 % / Description: rod / needle
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.0, 0.2 M MgCl2, 25% (W/Vol) PEG6000

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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: Oct 16, 2014 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91843 Å / Relative weight: 1
ReflectionResolution: 2.57→75.25 Å / Num. obs: 42814 / % possible obs: 97.9 % / Observed criterion σ(I): 1.7 / Redundancy: 2 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 4.4
Reflection shellResolution: 2.57→2.66 Å / Redundancy: 2 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 1.7 / % possible all: 92.6

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Processing

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

3dki


Resolution: 2.57→75.25 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.871 / SU B: 13.845 / SU ML: 0.292 / Cross valid method: THROUGHOUT / ESU R: 0.785 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26527 2176 5.1 %RANDOM
Rwork0.20118 ---
obs0.20445 40602 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.716 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å2-0.38 Å2-0.12 Å2
2--0.55 Å2-1.22 Å2
3---1.74 Å2
Refinement stepCycle: LAST / Resolution: 2.57→75.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8771 0 81 263 9115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199021
X-RAY DIFFRACTIONr_bond_other_d0.0020.028629
X-RAY DIFFRACTIONr_angle_refined_deg1.541.98812278
X-RAY DIFFRACTIONr_angle_other_deg0.8363.00219730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36751145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50822.807367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.756151367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9961582
X-RAY DIFFRACTIONr_chiral_restr0.0790.21389
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110273
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022037
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_it1.6763.1834622
X-RAY DIFFRACTIONr_mcbond_other1.6763.1834621
X-RAY DIFFRACTIONr_mcangle_it2.7184.7645753
X-RAY DIFFRACTIONr_mcangle_other2.7184.7655754
X-RAY DIFFRACTIONr_scbond_it1.8073.4014399
X-RAY DIFFRACTIONr_scbond_other1.8073.44400
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9525.0236526
X-RAY DIFFRACTIONr_long_range_B_refined5.75829.9938828
X-RAY DIFFRACTIONr_long_range_B_other5.75829.9938829
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.57→2.637 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 165 -
Rwork0.288 2950 -
obs--97.74 %

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