[English] 日本語
Yorodumi
- PDB-2yb4: Structure of an amidohydrolase from Chromobacterium violaceum (EF... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yb4
TitleStructure of an amidohydrolase from Chromobacterium violaceum (EFI target EFI-500202) with bound SO4, no metal
ComponentsAMIDOHYDROLASE
KeywordsHYDROLASE / ENZYME FUNCTION INITIATIVE / COG0613
Function / homology
Function and homology information


3',5'-nucleoside bisphosphate phosphatase / 3',5'-nucleotide bisphosphate phosphatase activity / 5'-3' RNA exonuclease activity / 5'-3' DNA exonuclease activity / dephosphorylation / manganese ion binding / nucleotide binding
Similarity search - Function
: / DNA polymerase; domain 1 - #650 / PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / Metal-dependent hydrolases / DNA polymerase; domain 1 / TIM Barrel ...: / DNA polymerase; domain 1 - #650 / PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / Metal-dependent hydrolases / DNA polymerase; domain 1 / TIM Barrel / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3',5'-nucleoside bisphosphate phosphatase
Similarity search - Component
Biological speciesCHROMOBACTERIUM VIOLACEUM (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.2 Å
AuthorsVetting, M.W. / Hillerich, B. / Foti, R. / Seidel, R.D. / Zencheck, W.D. / Toro, R. / Imker, H.J. / Raushel, F.M. / Gerlt, J.A. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2014
Title: Prospecting for Unannotated Enzymes: Discovery of a 3',5'-Nucleotide Bisphosphate Phosphatase within the Amidohydrolase Superfamily.
Authors: Cummings, J.A. / Vetting, M.W. / Ghodge, S.V. / Xu, C. / Hillerich, B. / Seidel, R.D. / Almo, S.C. / Raushel, F.M.
History
DepositionMar 1, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references / Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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: AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5593
Polymers31,3661
Non-polymers1922
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.070, 46.530, 130.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein AMIDOHYDROLASE


Mass: 31366.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHROMOBACTERIUM VIOLACEUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q7NXD4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC-TERMINAL TAG ON EXPRESSED PROTEIN AENLYFQSHHHHHHW SHPQFEK PROTEIN AS CRYSTALLIZED CLEAVED, LOSS ...C-TERMINAL TAG ON EXPRESSED PROTEIN AENLYFQSHHHHHHW SHPQFEK PROTEIN AS CRYSTALLIZED CLEAVED, LOSS OF SHHHHHHW SHPQFEK

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growpH: 6.1
Details: PROTEIN (15 MG/ML IN 10 MM HEPES PH 7.5, 150 MM NACL, 10% GLYCEROL) ADDED TO 25% PEG 3350, 100 MM BIS-TRIS PH 6.1, 200 MM AMSO4. CRYOSOLUTION WAS RESERVOIR WITH 20% ETHYLENE GLYCOL

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→46 Å / Num. obs: 12953 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 12.86 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.8 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.2→31.775 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 20.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 610 4.9 %
Rwork0.1704 --
obs0.1735 12440 95.74 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.201 Å2 / ksol: 0.381 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.5437 Å20 Å20 Å2
2--0.8447 Å20 Å2
3---4.8597 Å2
Refinement stepCycle: LAST / Resolution: 2.2→31.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 0 10 194 2340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062193
X-RAY DIFFRACTIONf_angle_d1.0532974
X-RAY DIFFRACTIONf_dihedral_angle_d12.318782
X-RAY DIFFRACTIONf_chiral_restr0.087319
X-RAY DIFFRACTIONf_plane_restr0.005395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.42130.25451470.17732795X-RAY DIFFRACTION93
2.4213-2.77150.27981490.17752894X-RAY DIFFRACTION95
2.7715-3.49110.24021510.16983006X-RAY DIFFRACTION98
3.4911-31.77840.19551630.16423135X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0648-0.0052-0.04160.0186-0.01720.07510.00870.00170.02430.00620.0104-0.003-0.0236-0.00230.06720.00910.00520.0087-0.0199-0.0234-0.020123.903418.384345.6312
20.0115-0.0021-0.00770.0558-0.00540.0166-0.0015-0.0092-0.0048-0.0053-0.0016-0.03490.0030.00920.0030.02820.0216-0.0070.021-0.00850.025226.458336.096741.7402
30.0639-0.01850.00030.0308-0.0160.09-0.01740.00810.0030.0075-0.001-0.0025-0.0115-0.0005-0.05610.0161-0.00210.00060.0215-0.00810.014628.443520.049759.3748
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:85)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 86:182)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 183:283)

+
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://pdbjlc1.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