[English] 日本語
Yorodumi
- PDB-5a6t: 1.65 A resolution Sulphite inhibited Sporosarcina pasteurii urease -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5a6t
Title1.65 A resolution Sulphite inhibited Sporosarcina pasteurii urease
Components(UREASE SUBUNIT ...) x 3
KeywordsHYDROLASE / UREASE / NICKEL / METALLOENZYME / SULFITE
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
NICKEL (II) ION / SULFITE ION / Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesSPOROSARCINA PASTEURII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMazzei, L. / Cianci, M. / Benini, S. / Bertini, L. / Musiani, F. / Ciurli, S.
CitationJournal: J.Inorg.Biochem. / Year: 2015
Title: Kinetic and Structural Studies Reveal a Unique Binding Mode of Sulfite to the Nickel Center in Urease.
Authors: Mazzei, L. / Cianci, M. / Benini, S. / Bertini, L. / Musiani, F. / Ciurli, S.
History
DepositionJul 1, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_label_seq_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.ptnr3_label_seq_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)87,41414
Polymers86,6863
Non-polymers72811
Water11,440635
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)262,24242
Polymers260,0589
Non-polymers2,18433
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area53630 Å2
ΔGint-232.1 kcal/mol
Surface area59180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.262, 131.262, 189.072
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

-
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 / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Source: (natural) SPOROSARCINA PASTEURII (bacteria) / References: UniProt: P41022, urease
#2: Protein UREASE SUBUNIT BETA / / UREA AMIDOHYDROLASE SUBUNIT BETA


Mass: 13975.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) / 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 / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Source: (natural) SPOROSARCINA PASTEURII (bacteria) / References: UniProt: P41020, urease

-
Non-polymers , 5 types, 646 molecules

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


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / 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-SO3 / SULFITE ION / Sulfite


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 635 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsFIRST FOUR RESIDUES OF THE SEQUENCE OF CHAIN B ARE MISSING IN THE STRUCTURE. ACCORDING TO THE DNA ...FIRST FOUR RESIDUES OF THE SEQUENCE OF CHAIN B ARE MISSING IN THE STRUCTURE. ACCORDING TO THE DNA SEQUENCE DEPOSITED WITH GENBANK ACCESSION NUMBER KR133628, THESE RESIDUES ARE NOT IN CONFLICT.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.23 % / Description: NONE
Crystal growpH: 6.3
Details: 1.8 M AMMONIUM SULFATE, 50 MM SODIUM CITRATE BUFFER PH 6.3, 50 MM SODIUM SULFITE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.033
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.65→72.69 Å / Num. obs: 115020 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 21.5 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 29.4
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 5.7 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AC7

4ac7


Resolution: 1.65→113.68 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.155 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.15246 5779 5 %RANDOM
Rwork0.12869 ---
obs0.12989 109132 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.624 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20.31 Å20 Å2
2--0.61 Å20 Å2
3----1.98 Å2
Refinement stepCycle: LAST / Resolution: 1.65→113.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6046 0 39 635 6720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0196349
X-RAY DIFFRACTIONr_bond_other_d0.0010.026128
X-RAY DIFFRACTIONr_angle_refined_deg2.0671.978592
X-RAY DIFFRACTIONr_angle_other_deg0.952314158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5785828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85725.018279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.018151110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.111537
X-RAY DIFFRACTIONr_chiral_restr0.1420.2965
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217262
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021341
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_it1.6331.643238
X-RAY DIFFRACTIONr_mcbond_other1.6311.643237
X-RAY DIFFRACTIONr_mcangle_it2.2482.4544066
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8441.9163111
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.181 383 -
Rwork0.16 7933 -
obs--98.98 %

+
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