[English] 日本語
Yorodumi
- PDB-5iwc: Mycobacterium tuberculosis CysM in complex with the Urea-scaffold... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5iwc
TitleMycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 3 [4-(3-([1,1'-Biphenyl]-3-yl)ureido)-2-hydroxybenzoic acid]
ComponentsO-phosphoserine sulfhydrylase
KeywordsLYASE / Mycobacterium tuberculosis / Cysteine biosynthesis / sulphur metabolism / 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 / 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-6EQ / PYRIDOXAL-5'-PHOSPHATE / O-phosphoserine sulfhydrylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSchnell, R. / Maric, S. / Lindqvist, Y. / Schneider, G.
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,6396
Polymers69,4482
Non-polymers1,1914
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-14 kcal/mol
Surface area23270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.040, 87.530, 98.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 2 - 317 / Label seq-ID: 5 - 320

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
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: Mutation: T2A, Lys51 covalent modification with PLP
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: cysM, Rv1336, MTCY130.21 / Plasmid: pET28a
Details (production host): N-terminal His6-tah, 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 / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-6EQ / 4-{[([1,1'-biphenyl]-3-yl)carbamoyl]amino}-2-hydroxybenzoic acid


Mass: 348.352 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H16N2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.15 % / Description: rod / needle
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 0.2M NH4-acetate, 25% PEG 3350

-
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: 2.7→66.04 Å / Num. obs: 15620 / % possible obs: 96.9 % / Observed criterion σ(I): 2.1 / Redundancy: 5 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 9.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 2.1 / % possible all: 95.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3dki

3dki


Resolution: 2.7→65.43 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.889 / SU B: 15.982 / SU ML: 0.327 / Cross valid method: THROUGHOUT / ESU R Free: 0.412 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26632 782 5 %RANDOM
Rwork0.2097 ---
obs0.21262 14795 96.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.24 Å2
Baniso -1Baniso -2Baniso -3
1-3.5 Å20 Å2-0 Å2
2---2.49 Å20 Å2
3----1.02 Å2
Refinement stepCycle: 1 / Resolution: 2.7→65.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4444 0 82 36 4562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194630
X-RAY DIFFRACTIONr_bond_other_d0.0040.024404
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.9926307
X-RAY DIFFRACTIONr_angle_other_deg1.1663.00310077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4025588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26322.857189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.36115699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6951542
X-RAY DIFFRACTIONr_chiral_restr0.0740.2713
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215281
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021045
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_it4.215.5892367
X-RAY DIFFRACTIONr_mcbond_other4.1965.5862366
X-RAY DIFFRACTIONr_mcangle_it6.6828.3562950
X-RAY DIFFRACTIONr_mcangle_other6.6818.3582951
X-RAY DIFFRACTIONr_scbond_it3.7685.9292263
X-RAY DIFFRACTIONr_scbond_other3.7685.9282264
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1888.7743358
X-RAY DIFFRACTIONr_long_range_B_refined9.99244.595099
X-RAY DIFFRACTIONr_long_range_B_other9.99144.595100
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 34310 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 38 -
Rwork0.282 1045 -
obs--92.09 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more