[English] 日本語
Yorodumi
- PDB-6zo1: 1.61 A resolution 3,5-dimethylcatechol (3,5-dimethylbenzene-1,2-d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zo1
Title1.61 A resolution 3,5-dimethylcatechol (3,5-dimethylbenzene-1,2-diol) inhibited Sporosarcina pasteurii urease
Components(Urease subunit ...) x 3
KeywordsMETAL BINDING PROTEIN / urease / nickel / enzyme / inhibitor
Function / homology
Function and homology information


urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm
Similarity search - Function
Urease, gamma subunit / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit / Urease, alpha subunit / Urease alpha subunit, C-terminal / Urease, beta subunit superfamily / Urease beta subunit ...Urease, gamma subunit / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit / Urease, alpha subunit / Urease alpha subunit, C-terminal / Urease, beta subunit superfamily / Urease beta subunit / Urease domain profile. / Urease alpha-subunit, N-terminal domain / Urease alpha-subunit, N-terminal domain / Urease, gamma/gamma-beta subunit / Urease, gamma subunit superfamily / Urease, gamma subunit / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
NICKEL (II) ION / HYDROXIDE ION / Urease subunit gamma / Urease subunit alpha / Urease subunit alpha / Urease subunit beta
Similarity search - Component
Biological speciesSporosarcina pasteurii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsMazzei, L. / Cianci, M. / Musiani, F. / Ciurli, S.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Inhibition of Urease, a Ni-Enzyme: The Reactivity of a Key Thiol With Mono- and Di-Substituted Catechols Elucidated by Kinetic, Structural, and Theoretical Studies.
Authors: Mazzei, L. / Contaldo, U. / Musiani, F. / Cianci, M. / Bagnolini, G. / Roberti, M. / Ciurli, S.
History
DepositionJul 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jan 31, 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: Urease subunit gamma
BBB: Urease subunit beta
CCC: Urease subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,75150
Polymers86,3763
Non-polymers3,37547
Water10,215567
1
AAA: Urease subunit gamma
BBB: Urease subunit beta
CCC: Urease subunit alpha
hetero molecules

AAA: Urease subunit gamma
BBB: Urease subunit beta
CCC: Urease subunit alpha
hetero molecules

AAA: Urease subunit gamma
BBB: Urease subunit beta
CCC: Urease subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,253150
Polymers259,1279
Non-polymers10,126141
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area71400 Å2
ΔGint-628 kcal/mol
Surface area61480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.566, 131.566, 188.919
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11CCC-624-

SO4

21CCC-787-

HOH

31CCC-1010-

HOH

-
Components

-
Urease subunit ... , 3 types, 3 molecules AAABBBCCC

#1: Protein Urease subunit gamma / / Urea amidohydrolase subunit gamma


Mass: 11134.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / References: UniProt: A0A0H3YGY5, urease
#2: Protein Urease subunit beta / / Urea amidohydrolase subunit beta


Mass: 13529.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / References: UniProt: P41021, urease
#3: Protein Urease subunit alpha / / Urea amidohydrolase subunit alpha


Mass: 61711.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria)
References: UniProt: A0A0H3YL32, UniProt: P41020*PLUS, urease

-
Non-polymers , 5 types, 614 molecules

#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#7: Chemical ChemComp-OH / HYDROXIDE ION / Hydroxide


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.76 Å3/Da / Density % sol: 55.45 % / Description: Rice shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 50 mM citrate buffer at pH 6.3, containing 1.6 - 2.0 M ammonium sulfate as a precipitant

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2017
RadiationMonochromator: Si(111)Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.61→45.49 Å / Num. obs: 123908 / % possible obs: 99.8 % / Redundancy: 8.7 % / Biso Wilson estimate: 21.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.05 / Rrim(I) all: 0.109 / Net I/σ(I): 12.4
Reflection shellResolution: 1.61→1.64 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.659 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6001 / CC1/2: 0.61 / Rpim(I) all: 0.845 / Rrim(I) all: 1.867 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G4H

5g4h


Resolution: 1.61→45.49 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.536 / SU ML: 0.05 / Cross valid method: FREE R-VALUE / ESU R: 0.063 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.159 6228 5.027 %
Rwork0.1357 117658 -
all0.137 --
obs-123886 99.637 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.786 Å20.393 Å20 Å2
2--0.786 Å2-0 Å2
3----2.549 Å2
Refinement stepCycle: LAST / Resolution: 1.61→45.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6041 0 210 567 6818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136594
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176197
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.6578910
X-RAY DIFFRACTIONr_angle_other_deg1.4991.61314423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9765850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94122.988328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.753151135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7151540
X-RAY DIFFRACTIONr_chiral_restr0.0980.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027400
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021260
X-RAY DIFFRACTIONr_nbd_refined0.2130.21304
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.26033
X-RAY DIFFRACTIONr_nbtor_refined0.1650.23130
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22982
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2483
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0870.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2570.262
X-RAY DIFFRACTIONr_nbd_other0.210.2261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1840.261
X-RAY DIFFRACTIONr_mcbond_it1.7652.2723296
X-RAY DIFFRACTIONr_mcbond_other1.7652.2723295
X-RAY DIFFRACTIONr_mcangle_it2.4193.3984147
X-RAY DIFFRACTIONr_mcangle_other2.4193.3994148
X-RAY DIFFRACTIONr_scbond_it3.7772.783295
X-RAY DIFFRACTIONr_scbond_other3.2682.6893236
X-RAY DIFFRACTIONr_scangle_it5.2413.994749
X-RAY DIFFRACTIONr_scangle_other4.7193.8494660
X-RAY DIFFRACTIONr_lrange_it6.66428.8977290
X-RAY DIFFRACTIONr_lrange_other6.66428.8957290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.6520.2694000.268605X-RAY DIFFRACTION99.6128
1.652-1.6970.244460.248377X-RAY DIFFRACTION99.9887
1.697-1.7460.214420.2078152X-RAY DIFFRACTION99.8954
1.746-1.80.2194280.1937952X-RAY DIFFRACTION99.9285
1.8-1.8590.2084340.1737675X-RAY DIFFRACTION99.9384
1.859-1.9240.1784190.1547420X-RAY DIFFRACTION99.949
1.924-1.9970.1663560.147239X-RAY DIFFRACTION99.9868
1.997-2.0780.1643790.1286933X-RAY DIFFRACTION99.9863
2.078-2.1710.1513320.1186689X-RAY DIFFRACTION99.9573
2.171-2.2770.1553680.1126377X-RAY DIFFRACTION99.8963
2.277-2.40.143290.1076075X-RAY DIFFRACTION99.8908
2.4-2.5450.1532890.1215781X-RAY DIFFRACTION99.7699
2.545-2.7210.1512900.1235403X-RAY DIFFRACTION99.5628
2.721-2.9390.1532590.1235087X-RAY DIFFRACTION99.6087
2.939-3.2190.1592400.1324694X-RAY DIFFRACTION99.5159
3.219-3.5990.1422190.1234250X-RAY DIFFRACTION99.1349
3.599-4.1550.1131970.113764X-RAY DIFFRACTION98.6305
4.155-5.0870.1371730.1083200X-RAY DIFFRACTION98.1951
5.087-7.1870.161450.1492514X-RAY DIFFRACTION97.8293
7.187-80.179830.1761472X-RAY DIFFRACTION95.5747

+
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