[English] 日本語
Yorodumi
- PDB-6qdy: The crystal structure of Sporosarcina pasteurii urease in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qdy
TitleThe crystal structure of Sporosarcina pasteurii urease in complex with its substrate urea
Components(Urease subunit ...) x 3
KeywordsHYDROLASE / urease / Sporosarcina pasteurii / nickel / urea
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
FLUORIDE ION / NICKEL (II) ION / UREA / 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: 1.416 Å
AuthorsMazzei, L. / Cianci, M. / Benini, S. / Ciurli, S.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: The Structure of the Elusive Urease-Urea Complex Unveils the Mechanism of a Paradigmatic Nickel-Dependent Enzyme.
Authors: Mazzei, L. / Cianci, M. / Benini, S. / Ciurli, S.
History
DepositionJan 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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_asym_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

-
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)87,31120
Polymers86,2403
Non-polymers1,07117
Water15,709872
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)261,93360
Polymers258,7199
Non-polymers3,21451
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 area58480 Å2
ΔGint-261 kcal/mol
Surface area57730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.565, 131.565, 188.683
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-1034-

HOH

21C-1042-

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)
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) / 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)
References: UniProt: A0A0H3YL32, UniProt: P41020*PLUS, urease

-
Non-polymers , 6 types, 889 molecules

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


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NI / NICKEL (II) ION


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


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#8: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2O
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 872 / 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: 2.75 Å3/Da / Density % sol: 55.34 % / Description: Rice-shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 1.8 M ammonium sulfate, 100 mM citrate pH 6.3, 100 mM sodium fluoride, 200 mM urea
PH range: 6.5-7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9672 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2018
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9672 Å / Relative weight: 1
ReflectionResolution: 1.416→113.94 Å / Num. obs: 177668 / % possible obs: 98.1 % / Redundancy: 19.3 % / Biso Wilson estimate: 8.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.028 / Rrim(I) all: 0.092 / Net I/σ(I): 25
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6361 / CC1/2: 0.709 / Rpim(I) all: 0.375 / Rrim(I) all: 0.893 / % possible all: 72.4

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OL4

5ol4


Resolution: 1.416→97.535 Å / SU ML: 0.08 / SU R Cruickshank DPI: 0.0345 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 9.38
RfactorNum. reflection% reflection
Rfree0.1191 8928 5.03 %
Rwork0.095 --
obs0.0962 177610 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 13.757 Å2
Refinement stepCycle: LAST / Resolution: 1.416→97.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6046 0 61 880 6987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076580
X-RAY DIFFRACTIONf_angle_d1.0468927
X-RAY DIFFRACTIONf_dihedral_angle_d13.8012502
X-RAY DIFFRACTIONf_chiral_restr0.086984
X-RAY DIFFRACTIONf_plane_restr0.0071196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4165-1.43260.2772080.25293591X-RAY DIFFRACTION64
1.4326-1.44940.18152720.14695189X-RAY DIFFRACTION92
1.4494-1.46710.13972990.1185461X-RAY DIFFRACTION97
1.4671-1.48570.14522620.10585547X-RAY DIFFRACTION97
1.4857-1.50520.12983110.09135579X-RAY DIFFRACTION99
1.5052-1.52590.11942900.08585617X-RAY DIFFRACTION99
1.5259-1.54770.1223040.0865618X-RAY DIFFRACTION99
1.5477-1.57080.12432930.08785624X-RAY DIFFRACTION99
1.5708-1.59530.11792920.08245626X-RAY DIFFRACTION99
1.5953-1.62150.1113230.07855600X-RAY DIFFRACTION99
1.6215-1.64940.11122920.07975668X-RAY DIFFRACTION99
1.6494-1.67940.1243050.08315629X-RAY DIFFRACTION99
1.6794-1.71170.1112710.07775685X-RAY DIFFRACTION99
1.7117-1.74670.10542920.07355657X-RAY DIFFRACTION99
1.7467-1.78470.10652950.07675701X-RAY DIFFRACTION100
1.7847-1.82620.11443160.07725697X-RAY DIFFRACTION100
1.8262-1.87180.09823130.07535638X-RAY DIFFRACTION100
1.8718-1.92250.11473090.07815690X-RAY DIFFRACTION100
1.9225-1.9790.11023030.07925702X-RAY DIFFRACTION100
1.979-2.04290.11112870.07965715X-RAY DIFFRACTION100
2.0429-2.11590.10692880.08045757X-RAY DIFFRACTION100
2.1159-2.20070.10632970.07865748X-RAY DIFFRACTION100
2.2007-2.30080.09172970.07665759X-RAY DIFFRACTION100
2.3008-2.42210.0993170.07875753X-RAY DIFFRACTION100
2.4221-2.57390.10843250.08545750X-RAY DIFFRACTION100
2.5739-2.77270.11592840.09325830X-RAY DIFFRACTION100
2.7727-3.05170.10913180.10625829X-RAY DIFFRACTION100
3.0517-3.49330.12423410.1085827X-RAY DIFFRACTION100
3.4933-4.40120.11712990.0995964X-RAY DIFFRACTION100
4.4012-97.7670.16283250.1436231X-RAY DIFFRACTION100

+
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://pdbjlvh1.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