[English] 日本語
Yorodumi
- PDB-4s2o: OXA-10 in complex with Avibactam -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4s2o
TitleOXA-10 in complex with Avibactam
ComponentsBeta-lactamase OXA-10
Keywordshydrolase/antibiotic / hydrolase-antibiotic complex
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic
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
: / Chem-NXL / Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKing, D.T. / Strynadka, N.C.J.
CitationJournal: ACS Infect Dis / Year: 2015
Title: Molecular Mechanism of Avibactam-Mediated beta-Lactamase Inhibition.
Authors: King, D.T. / King, A.M. / Lal, S.M. / Wright, G.D. / Strynadka, N.C.
History
DepositionJan 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Non-polymer description
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

-
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)55,8198
Polymers55,0492
Non-polymers7706
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-46 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.600, 96.500, 125.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A21 - 264
2010B21 - 264
DetailsThis protein behaves as a dimer in solution

-
Components

#1: Protein Beta-lactamase OXA-10 / Beta-lactamase PSE-2


Mass: 27524.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bla, oxa10, pse2 / Production host: Escherichia coli (E. coli) / References: UniProt: P14489, beta-lactamase
#2: Chemical ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form, NXL104, bound form


Mass: 267.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13N3O6S / Comment: antibiotic, inhibitor*YM
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.8 M (NH4)2SO4, 0.1 M MES pH 6.5, 10 mM CoCl2, 2mM avibactam, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 13, 2013
RadiationMonochromator: double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→52.66 Å / Num. all: 65809 / Num. obs: 64493 / % possible obs: 98 %
Reflection shellResolution: 1.7→1.73 Å / % possible all: 99.9

-
Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
REFMAC5.8.0071refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→52.66 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.239 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22988 3223 5 %RANDOM
Rwork0.18446 ---
obs0.1867 61211 97.73 %-
all-62460 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.477 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2--0.91 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.7→52.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3876 0 38 438 4352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.024049
X-RAY DIFFRACTIONr_bond_other_d0.0030.023865
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.9495482
X-RAY DIFFRACTIONr_angle_other_deg1.17938923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9585501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00425.281178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93115724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8951515
X-RAY DIFFRACTIONr_chiral_restr0.1150.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024608
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02919
X-RAY DIFFRACTIONr_mcbond_it4.3021.7781998
X-RAY DIFFRACTIONr_mcbond_other4.2811.7751996
X-RAY DIFFRACTIONr_mcangle_it4.9212.6552501
X-RAY DIFFRACTIONr_mcangle_other4.8952.6552501
X-RAY DIFFRACTIONr_scbond_it5.4372.2192051
X-RAY DIFFRACTIONr_scbond_other5.4362.2192052
X-RAY DIFFRACTIONr_scangle_other6.0983.1552982
X-RAY DIFFRACTIONr_long_range_B_refined6.24616.6865172
X-RAY DIFFRACTIONr_long_range_B_other6.07515.9914949
X-RAY DIFFRACTIONr_rigid_bond_restr6.1637914
X-RAY DIFFRACTIONr_sphericity_free28.1655153
X-RAY DIFFRACTIONr_sphericity_bonded12.64858141
Refine LS restraints NCS

Ens-ID: 1 / Number: 14888 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 240 -
Rwork0.141 4597 -
obs--99.61 %
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)
112.6457-1.90757.11653.3939-0.25614.2215-0.24810.34451.1074-0.3959-0.3328-0.3256-0.26470.1240.58090.1391-0.0099-0.00230.11480.09440.147219.73175.1685-17.3468
20.3109-0.133-0.02840.293-0.08360.6362-0.03440.0080.02030.00680.01790.0067-0.0479-0.01390.01660.04010.0003-0.00110.0353-0.00090.011911.3681-10.89790.737
31.5885-1.7311-0.08142.00450.21061.0795-0.03980.0550.20190.03020.003-0.2197-0.17890.12670.03680.077-0.0291-0.02430.03980.01410.044521.6292-1.8151-5.5439
40.24550.0521-0.00990.6480.54461.75250.0425-0.08530.1408-0.015-0.05760.0601-0.06860.07020.01510.0324-0.01480.01910.0433-0.05030.083612.43688.927127.3975
51.3208-1.40321.41767.64250.75074.5916-0.16530.06310.5799-0.1597-0.1855-0.6419-0.62950.2390.35080.28280.0045-0.02790.07820.02520.29529.532121.275211.5358
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 31
2X-RAY DIFFRACTION2A32 - 211
3X-RAY DIFFRACTION3A212 - 265
4X-RAY DIFFRACTION4B20 - 94
5X-RAY DIFFRACTION5B95 - 118

+
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