[English] 日本語
Yorodumi
- PDB-6rkg: 1.32 A RESOLUTION OF SPOROSARCINA PASTEURII UREASE INHIBITED IN T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rkg
Title1.32 A RESOLUTION OF SPOROSARCINA PASTEURII UREASE INHIBITED IN THE PRESENCE OF NBPTO AT pH 7.5
Components(Urease subunit ...) x 3
KeywordsHYDROLASE / UREA / NICKEL / NBPTO
Function / homology
Function and homology information


urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm
Similarity search - Function
Urease, subunit B / Urease, beta subunit / Urease; subunit A / Urease, gamma-like subunit / Urease, gamma subunit / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit ...Urease, subunit B / Urease, beta subunit / Urease; subunit A / Urease, gamma-like 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 / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Ribbon / Roll / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DIAMIDOPHOSPHATE / NICKEL (II) ION / Urease subunit gamma / Urease subunit alpha / Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesSporosarcina pasteurii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsMazzei, L. / Cianci, M. / Benini, S. / Ciurli, S.
CitationJournal: Chemistry / Year: 2019
Title: The Impact of pH on Catalytically Critical Protein Conformational Changes: The Case of the Urease, a Nickel Enzyme.
Authors: Mazzei, L. / Cianci, M. / Benini, S. / Ciurli, S.
History
DepositionApr 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_conn
Item: _pdbx_distant_solvent_atoms.auth_asym_id / _pdbx_distant_solvent_atoms.auth_seq_id ..._pdbx_distant_solvent_atoms.auth_asym_id / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_struct_assembly_gen.assembly_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Jan 24, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Urease subunit gamma
B: Urease subunit beta
C: Urease subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,14730
Polymers86,2403
Non-polymers1,90727
Water13,313739
1
A: Urease subunit gamma
B: Urease subunit beta
C: Urease subunit alpha
hetero molecules

A: Urease subunit gamma
B: Urease subunit beta
C: Urease subunit alpha
hetero molecules

A: Urease subunit gamma
B: Urease subunit beta
C: Urease subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,44090
Polymers258,7199
Non-polymers5,72181
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
Unit cell
Length a, b, c (Å)131.783, 131.783, 188.768
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11C-619-

SO4

21C-619-

SO4

31C-620-

SO4

41C-1010-

HOH

51C-1019-

HOH

-
Components

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

#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) / Variant: DSM33
References: UniProt: A0A0H3YGY5, UniProt: P41022*PLUS, 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) / Variant: DSM33 / References: UniProt: P41021, urease
#3: Protein Urease subunit alpha / / Urea amidohydrolase subunit alpha


Mass: 61575.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / Variant: DSM33
References: UniProt: A0A0H3YL32, UniProt: P41020*PLUS, urease

-
Non-polymers , 5 types, 766 molecules

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


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / 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-2PA / DIAMIDOPHOSPHATE / Diamidophosphate


Mass: 96.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5N2O2P
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 739 / 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: 2.76 Å3/Da / Density % sol: 55.51 % / Description: Rice-shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein dissolved in 50 mM HEPES, pH 7.5, 2 mM EDTA, 4 mM NBPTO. Precipitant solution consisting of 100 mM citrate buffer, 1.7-1.9 M ammonium sulfate, 4 mM NBPTO, at pH 7.5.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2018
RadiationMonochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.32→97.67 Å / Num. obs: 221217 / % possible obs: 98.8 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.035 / Rrim(I) all: 0.128 / Net I/σ(I): 13.3
Reflection shellResolution: 1.32→1.34 Å / Redundancy: 13.8 % / Rmerge(I) obs: 2.23 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 10653 / CC1/2: 0.653 / Rpim(I) all: 0.633 / Rrim(I) all: 2.392 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OL4

5ol4


Resolution: 1.32→97.67 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.981 / SU B: 1.587 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.035 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14254 11101 5 %RANDOM
Rwork0.1217 ---
obs0.12275 210078 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.396 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.46 Å2
Refinement stepCycle: 1 / Resolution: 1.32→97.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6046 0 109 741 6896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196491
X-RAY DIFFRACTIONr_bond_other_d0.0010.026261
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9778783
X-RAY DIFFRACTIONr_angle_other_deg0.795314460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2445842
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38924.929282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.708151125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6591539
X-RAY DIFFRACTIONr_chiral_restr0.0820.2977
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217449
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021377
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_it1.5561.3613302
X-RAY DIFFRACTIONr_mcbond_other1.5571.3613301
X-RAY DIFFRACTIONr_mcangle_it1.9412.0524166
X-RAY DIFFRACTIONr_mcangle_other1.9412.0524167
X-RAY DIFFRACTIONr_scbond_it5.1741.6763189
X-RAY DIFFRACTIONr_scbond_other5.1571.6663178
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5812.3764600
X-RAY DIFFRACTIONr_long_range_B_refined4.63512.8647805
X-RAY DIFFRACTIONr_long_range_B_other4.63412.8677806
X-RAY DIFFRACTIONr_rigid_bond_restr2.304312750
X-RAY DIFFRACTIONr_sphericity_free32.8195160
X-RAY DIFFRACTIONr_sphericity_bonded12.692513230
LS refinement shellResolution: 1.32→1.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 779 -
Rwork0.239 15120 -
obs--97.18 %

+
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