[English] 日本語
Yorodumi
- PDB-5fq9: Crystal structure of the OXA10 with 1C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fq9
TitleCrystal structure of the OXA10 with 1C
ComponentsBETA-LACTAMASE OXA-10
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase / beta-lactamase activity / periplasmic space / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-C6S / Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBrem, J. / McDonough, M.A. / Cain, R. / Clifton, I. / Fishwick, C.W.G. / Schofield, C.J.
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis of metallo-beta-lactamase, serine-beta-lactamase and penicillin-binding protein inhibition by cyclic boronates.
Authors: Brem, J. / Cain, R. / Cahill, S. / McDonough, M.A. / Clifton, I.J. / Jimenez-Castellanos, J.C. / Avison, M.B. / Spencer, J. / Fishwick, C.W. / Schofield, C.J.
History
DepositionDec 8, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
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_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 / _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: BETA-LACTAMASE OXA-10
B: BETA-LACTAMASE OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,63111
Polymers55,5112
Non-polymers1,1209
Water8,845491
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-37.4 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.898, 103.109, 125.529
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8054, 0.591, 0.0452), (0.5907, -0.8066, 0.0216), (0.0492, 0.0093, -0.9987)
Vector: -2.545, 6.5599, 15.9364)

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein BETA-LACTAMASE OXA-10


Mass: 27755.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 1C BOUND TO THE ACTIVE SITE / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14489, beta-lactamase

-
Non-polymers , 6 types, 500 molecules

#2: Chemical ChemComp-C6S / (3R)-3-(cyclohexylcarbonylamino)-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid


Mass: 317.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20BNO5
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 3.17 Å3/Da / Density % sol: 61.15 % / Description: NONE
Crystal growpH: 5.5 / Details: 0.2M NACL, 0.1M NA ACETATE PH 5.0, 20% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2015 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→15.44 Å / Num. obs: 253261 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 5.6
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K6R

1k6r


Resolution: 1.5→15.424 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 17.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1806 5021 4.9 %
Rwork0.1569 --
obs0.158 102233 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.325 Å2
Refinement stepCycle: LAST / Resolution: 1.5→15.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3824 0 76 491 4391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144102
X-RAY DIFFRACTIONf_angle_d1.3445579
X-RAY DIFFRACTIONf_dihedral_angle_d21.3751527
X-RAY DIFFRACTIONf_chiral_restr0.094611
X-RAY DIFFRACTIONf_plane_restr0.01715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5170.3481580.31063226X-RAY DIFFRACTION100
1.517-1.53480.29921610.30343197X-RAY DIFFRACTION100
1.5348-1.55350.29811690.28273177X-RAY DIFFRACTION100
1.5535-1.57320.25671620.27533224X-RAY DIFFRACTION100
1.5732-1.59390.26311580.25333185X-RAY DIFFRACTION100
1.5939-1.61570.24831450.25033236X-RAY DIFFRACTION100
1.6157-1.63870.2411890.23483203X-RAY DIFFRACTION100
1.6387-1.66320.24351720.21833197X-RAY DIFFRACTION100
1.6632-1.68910.20491740.20833201X-RAY DIFFRACTION100
1.6891-1.71680.22771630.19523179X-RAY DIFFRACTION100
1.7168-1.74630.21931740.19133258X-RAY DIFFRACTION100
1.7463-1.77810.20711740.18443159X-RAY DIFFRACTION100
1.7781-1.81220.19121620.17673254X-RAY DIFFRACTION100
1.8122-1.84910.20391650.16713200X-RAY DIFFRACTION100
1.8491-1.88930.17971780.15973210X-RAY DIFFRACTION100
1.8893-1.93310.19491520.16143237X-RAY DIFFRACTION100
1.9331-1.98140.17011620.14553229X-RAY DIFFRACTION100
1.9814-2.03490.18841830.14533228X-RAY DIFFRACTION100
2.0349-2.09460.17741610.14313200X-RAY DIFFRACTION100
2.0946-2.1620.14731750.13633235X-RAY DIFFRACTION100
2.162-2.23910.15371860.13313232X-RAY DIFFRACTION100
2.2391-2.32840.16861550.13733289X-RAY DIFFRACTION100
2.3284-2.4340.18061610.13643232X-RAY DIFFRACTION100
2.434-2.56180.16741590.13753252X-RAY DIFFRACTION100
2.5618-2.72150.17231820.143263X-RAY DIFFRACTION100
2.7215-2.93030.17681720.14443265X-RAY DIFFRACTION100
2.9303-3.22270.20021500.15053303X-RAY DIFFRACTION100
3.2227-3.68350.16751540.14413335X-RAY DIFFRACTION100
3.6835-4.62010.13181640.12393340X-RAY DIFFRACTION100
4.6201-15.42430.16672010.1473466X-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://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