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- PDB-5iw8: Mycobacterium tuberculosis CysM in complex with the Urea-scaffold... -

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Basic information

Entry
Database: PDB / ID: 5iw8
TitleMycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 4 [5-(3-([1,1'-Biphenyl]-3-yl)ureido)-2-hydroxybenzoic 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 / 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 / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6EC / PYRIDOXAL-5'-PHOSPHATE / O-phosphoserine sulfhydrylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsBrunner, K. / Schnell, R. / 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
DepositionMar 22, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6627
Polymers69,4482
Non-polymers1,2145
Water8,035446
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-23 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.164, 87.883, 100.781
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
Source method: isolated from a genetically manipulated source
Details: T2A mutation. Lys51 covalent modification with PLP
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: cysM, Rv1336, MTCY130.21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P9WP53, [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase
#2: Chemical ChemComp-6EC / 5-{[([1,1'-biphenyl]-3-yl)carbamoyl]amino}-2-hydroxybenzoic acid


Mass: 348.352 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H16N2O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 2.13 Å3/Da / Density % sol: 42.16 % / Description: rod / needle
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES 6 pH 20 %w/v PEG 6K 0.2 M NH4Cl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2015 / Details: Si mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.04→55.95 Å / Num. obs: 38565 / % possible obs: 99.5 % / Observed criterion σ(I): 1.9 / Redundancy: 5.5 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 8.3
Reflection shellResolution: 2.04→2.15 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 1.9 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DKI

3dki


Resolution: 2.04→55.95 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.19 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.185 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23714 1857 4.8 %RANDOM
Rwork0.18446 ---
obs0.1871 36652 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.623 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å2-0 Å2
2---0.07 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.04→55.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4626 0 53 446 5125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194789
X-RAY DIFFRACTIONr_bond_other_d0.0020.024542
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.996525
X-RAY DIFFRACTIONr_angle_other_deg0.8353.00210389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9045616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.61522.857196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1815720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.251544
X-RAY DIFFRACTIONr_chiral_restr0.0790.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215516
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021090
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.039→2.092 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 137 -
Rwork0.288 2554 -
obs--94.55 %

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