[English] 日本語
Yorodumi
- PDB-6z4n: CRYSTAL STRUCTURE OF OASS COMPLEXED WITH UPAR INHIBITOR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z4n
TitleCRYSTAL STRUCTURE OF OASS COMPLEXED WITH UPAR INHIBITOR
ComponentsCysteine synthase A
KeywordsLYASE / CYSTEIN BIOSYNTHESIS / BETA REPLACEMENT ENZYME / PLP DEPENDENT ENZYME / HOMODIMER / INHIBITOR
Function / homology
Function and homology information


cysteine synthase / cystathionine beta-synthase activity / cysteine synthase activity / L-cysteine desulfhydrase activity / cysteine biosynthetic process from serine / cytoplasm
Similarity search - Function
Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme
Similarity search - Domain/homology
: / PYRIDOXAL-5'-PHOSPHATE / Chem-Q7B / Cysteine synthase A
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsDemitri, N. / Storici, P. / Campanini, B.
CitationJournal: Acs Infect Dis. / Year: 2021
Title: Investigational Studies on a Hit Compound Cyclopropane-Carboxylic Acid Derivative Targeting O -Acetylserine Sulfhydrylase as a Colistin Adjuvant.
Authors: Annunziato, G. / Spadini, C. / Franko, N. / Storici, P. / Demitri, N. / Pieroni, M. / Flisi, S. / Rosati, L. / Iannarelli, M. / Marchetti, M. / Magalhaes, J. / Bettati, S. / Mozzarelli, A. / ...Authors: Annunziato, G. / Spadini, C. / Franko, N. / Storici, P. / Demitri, N. / Pieroni, M. / Flisi, S. / Rosati, L. / Iannarelli, M. / Marchetti, M. / Magalhaes, J. / Bettati, S. / Mozzarelli, A. / Cabassi, C.S. / Campanini, B. / Costantino, G.
History
DepositionMay 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Cysteine synthase A
BBB: Cysteine synthase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,00813
Polymers69,4252
Non-polymers1,58311
Water15,655869
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-29 kcal/mol
Surface area23330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.261, 96.275, 140.835
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB) / NCS ensembles : (Details: Chains AAA BBB)

-
Components

-
Protein , 1 types, 2 molecules AAABBB

#1: Protein Cysteine synthase A / CSase A / O-acetylserine (thiol)-lyase A / OAS-TL A / O-acetylserine sulfhydrylase A


Mass: 34712.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Gene: cysK, STM2430 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A1E3, cysteine synthase

-
Non-polymers , 6 types, 880 molecules

#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-Q7B / (1~{S},2~{S})-1-[(4-methylphenyl)methyl]-2-phenyl-cyclopropane-1-carboxylic acid


Mass: 266.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 869 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.47 %
Description: Crystals grew within 5 days at 25C as monoclinic plates of 1.1 mm x 0.4 mm x 0.1 mm dimension. The crystals were soaked for 2 hours at RT in a solution containing 1mM UPAR, 32% (w/v) PEG ...Description: Crystals grew within 5 days at 25C as monoclinic plates of 1.1 mm x 0.4 mm x 0.1 mm dimension. The crystals were soaked for 2 hours at RT in a solution containing 1mM UPAR, 32% (w/v) PEG 4000, 150mM LiSO4, 100 mM Tris pH 7.0 and 5% glycerol (as cryoprotectant agent) and subsequently flash-frozen in N2(l) to be measured.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Drops contained 1 uL of 20 mg/mL StOASS-A mixed with 1 uL of reservoir solution containing 30-31% (w/v) PEG4000, 130-180 mM Li2SO4 (Fluka), 100 mM Tris base pH = 7.0.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 25, 2018
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→46.648 Å / Num. obs: 214538 / % possible obs: 94.35 % / Redundancy: 1.9 % / Biso Wilson estimate: 10.08 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0286 / Rpim(I) all: 0.0286 / Rrim(I) all: 0.04044 / Net I/σ(I): 10.89
Reflection shellResolution: 1.2→1.243 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.5601 / Mean I/σ(I) obs: 0.72 / Num. unique obs: 14933 / CC1/2: 0.569 / CC star: 0.852 / Rpim(I) all: 0.5601 / Rrim(I) all: 0.7921 / % possible all: 65.85

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OAS

1oas


Resolution: 1.2→46.648 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.116 / SU ML: 0.038 / Cross valid method: FREE R-VALUE / ESU R: 0.039 / ESU R Free: 0.039
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1787 10659 4.968 %
Rwork0.1542 203877 -
all0.155 --
obs-214536 94.96 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.357 Å2
Baniso -1Baniso -2Baniso -3
1--1.685 Å2-0 Å20 Å2
2--2.071 Å2-0 Å2
3----0.387 Å2
Refinement stepCycle: LAST / Resolution: 1.2→46.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4787 0 99 869 5755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0135375
X-RAY DIFFRACTIONr_bond_other_d0.0030.0175302
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.6597309
X-RAY DIFFRACTIONr_angle_other_deg1.5741.58712379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2625734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55723.077234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.585151017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.491531
X-RAY DIFFRACTIONr_chiral_restr0.1050.2743
X-RAY DIFFRACTIONr_chiral_restr_other1.9310.26
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025971
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021002
X-RAY DIFFRACTIONr_nbd_refined0.2210.21060
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.25019
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22561
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22305
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2461
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.6090.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0740.212
X-RAY DIFFRACTIONr_nbd_other0.1730.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1160.230
X-RAY DIFFRACTIONr_mcbond_it1.4571.5082708
X-RAY DIFFRACTIONr_mcbond_other1.4551.5082707
X-RAY DIFFRACTIONr_mcangle_it1.8892.2783407
X-RAY DIFFRACTIONr_mcangle_other1.892.2793408
X-RAY DIFFRACTIONr_scbond_it2.3241.7842667
X-RAY DIFFRACTIONr_scbond_other2.3161.7842667
X-RAY DIFFRACTIONr_scangle_it2.6742.5643859
X-RAY DIFFRACTIONr_scangle_other2.6742.5653860
X-RAY DIFFRACTIONr_lrange_it3.26818.7316108
X-RAY DIFFRACTIONr_lrange_other2.97418.4265987
X-RAY DIFFRACTIONr_rigid_bond_restr6.148310677
X-RAY DIFFRACTIONr_ncsr_local_group_10.10.0510107
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.2310.3185300.31410051X-RAY DIFFRACTION63.8756
1.231-1.2650.3136320.29612294X-RAY DIFFRACTION79.8098
1.265-1.3020.2686650.26813514X-RAY DIFFRACTION90.6006
1.302-1.3420.257260.23914190X-RAY DIFFRACTION97.5923
1.342-1.3860.2277440.20913949X-RAY DIFFRACTION99.6068
1.386-1.4340.2167000.19413636X-RAY DIFFRACTION99.7426
1.434-1.4880.2147300.17613074X-RAY DIFFRACTION99.7759
1.488-1.5490.1966780.16612617X-RAY DIFFRACTION99.8873
1.549-1.6180.1866070.14912180X-RAY DIFFRACTION99.8516
1.618-1.6970.1735550.13511660X-RAY DIFFRACTION99.9264
1.697-1.7890.1895970.13711044X-RAY DIFFRACTION99.9142
1.789-1.8970.1735320.12910539X-RAY DIFFRACTION99.8737
1.897-2.0280.165600.1289805X-RAY DIFFRACTION99.769
2.028-2.190.1484470.129226X-RAY DIFFRACTION99.7216
2.19-2.3990.144290.1158519X-RAY DIFFRACTION99.7992
2.399-2.6820.1454160.1067739X-RAY DIFFRACTION99.951
2.682-3.0960.1393700.126818X-RAY DIFFRACTION99.8611
3.096-3.7910.1583390.145811X-RAY DIFFRACTION99.9025
3.791-5.3550.1522520.1524569X-RAY DIFFRACTION99.855
5.355-46.6480.2871500.2752642X-RAY DIFFRACTION99.8212

+
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