[English] 日本語
Yorodumi
- PDB-5fqm: Last common ancestor of Gram Negative Bacteria (GNCA) Class A bet... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fqm
TitleLast common ancestor of Gram Negative Bacteria (GNCA) Class A beta- lactamase
ComponentsGNCA BETA LACTAMASE
KeywordsHYDROLASE / PRECAMBRIAN / RESURRECTED BETA-LACTAMASE / GNCA
Function / homologyBeta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMartinez Rodriguez, S. / Gavira, J.A. / Risso, V.A. / Sanchez Ruiz, J.M.
CitationJournal: Nat Commun / Year: 2017
Title: De novo active sites for resurrected Precambrian enzymes.
Authors: Risso, V.A. / Martinez-Rodriguez, S. / Candel, A.M. / Kruger, D.M. / Pantoja-Uceda, D. / Ortega-Munoz, M. / Santoyo-Gonzalez, F. / Gaucher, E.A. / Kamerlin, S.C.L. / Bruix, M. / Gavira, J.A. / Sanchez-Ruiz, J.M.
History
DepositionDec 12, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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 / 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: GNCA BETA LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,07413
Polymers28,9651
Non-polymers1,10912
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.230, 94.230, 93.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

-
Components

#1: Protein GNCA BETA LACTAMASE


Mass: 28964.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Description: RESURRECTED SEQUENCE, ANCESTRAL RECONSTRUCTED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS ENTRY IS RELEATED TO PDB ENTRIES 4UHU AND 4B88

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.32 % / Description: NONE
Crystal growpH: 8 / Details: 2.0M NH4SO4, 0.1M TRIS-HCL PH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.02
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.5→21.07 Å / Num. obs: 59525 / % possible obs: 91.3 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 3.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.1 / % possible all: 95.7

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B88

4b88


Resolution: 1.5→21.07 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 19.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1979 3112 5.2 %
Rwork0.176 --
obs0.1772 59484 91.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.05 Å2
Refinement stepCycle: LAST / Resolution: 1.5→21.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 71 311 2358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012227
X-RAY DIFFRACTIONf_angle_d1.393027
X-RAY DIFFRACTIONf_dihedral_angle_d15.316842
X-RAY DIFFRACTIONf_chiral_restr0.057337
X-RAY DIFFRACTIONf_plane_restr0.007401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.52350.27441680.25552773X-RAY DIFFRACTION99
1.5235-1.54840.2713870.24831735X-RAY DIFFRACTION62
1.5484-1.57510.29541510.25612739X-RAY DIFFRACTION99
1.5751-1.60380.24531530.22722789X-RAY DIFFRACTION99
1.6038-1.63460.2361670.21252769X-RAY DIFFRACTION100
1.6346-1.66790.25521760.20332785X-RAY DIFFRACTION100
1.6679-1.70420.2491480.19512790X-RAY DIFFRACTION99
1.7042-1.74380.22331170.18952820X-RAY DIFFRACTION100
1.7438-1.78740.21931730.18422749X-RAY DIFFRACTION99
1.7874-1.83570.19081400.1752824X-RAY DIFFRACTION100
1.8357-1.88970.18541150.17712518X-RAY DIFFRACTION99
1.8897-1.95060.1759760.16851375X-RAY DIFFRACTION60
1.9506-2.02030.1692880.16542264X-RAY DIFFRACTION100
2.0203-2.10110.1848830.16632246X-RAY DIFFRACTION79
2.1011-2.19670.21042150.16432749X-RAY DIFFRACTION99
2.1967-2.31230.17771380.17142233X-RAY DIFFRACTION80
2.3123-2.4570.17582140.17292746X-RAY DIFFRACTION100
2.457-2.64640.1661070.17362853X-RAY DIFFRACTION100
2.6464-2.91210.21021400.17032542X-RAY DIFFRACTION90
2.9121-3.3320.21281630.16882799X-RAY DIFFRACTION100
3.332-4.19260.17561580.14862397X-RAY DIFFRACTION85
4.1926-21.07250.18561350.17772877X-RAY DIFFRACTION100
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)
10.13120.074-0.18630.1352-0.01590.16110.0380.02260.0136-0.2764-0.0030.1268-0.1462-0.05850.07580.16740.0247-0.05610.1035-0.01930.1552-7.59225.2182-7.141
20.30530.246-0.08420.25790.0530.1222-0.1323-0.16770.00990.11370.129-0.05440.05620.13770.00670.15940.0661-0.00810.1701-0.00710.101617.614110.46746.5647
30.4545-0.2077-0.22690.52110.27220.3578-0.0333-0.0475-0.0149-0.01550.0083-0.01180.02810.033-0.0020.1080.00680.00570.0913-0.00820.09046.173915.1488-0.8701
40.114-0.1006-0.09160.19-0.12880.2582-0.01050.0230.0302-0.0672-0.01790.1517-0.0473-0.10910.1410.09930.0008-0.00390.1069-0.04120.1384-8.979121.70451.0731
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 28 THROUGH 68 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 69 THROUGH 118 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 119 THROUGH 258 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 259 THROUGH 292 )

+
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