[English] 日本語
Yorodumi
- PDB-5wae: ADC-7 in complex with boronic acid transition state inhibitor CR167 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wae
TitleADC-7 in complex with boronic acid transition state inhibitor CR167
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / inhibitor / Beta-lactamase / BATSI / ADC-7 / ANTIMICROBIAL PROTEIN / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-A1J / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.804 Å
AuthorsPowers, R.A. / Wallar, B.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI072219 United States
CitationJournal: ACS Infect Dis / Year: 2018
Title: Structure-Based Analysis of Boronic Acids as Inhibitors of Acinetobacter-Derived Cephalosporinase-7, a Unique Class C beta-Lactamase.
Authors: Bouza, A.A. / Swanson, H.C. / Smolen, K.A. / VanDine, A.L. / Taracila, M.A. / Romagnoli, C. / Caselli, E. / Prati, F. / Bonomo, R.A. / Powers, R.A. / Wallar, B.J.
History
DepositionJun 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,6468
Polymers163,2344
Non-polymers1,4124
Water10,557586
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1622
Polymers40,8081
Non-polymers3531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1622
Polymers40,8081
Non-polymers3531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1622
Polymers40,8081
Non-polymers3531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1622
Polymers40,8081
Non-polymers3531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.790, 81.045, 105.058
Angle α, β, γ (deg.)90.00, 113.45, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Beta-lactamase


Mass: 40808.496 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DRA1, beta-lactamase
#2: Chemical
ChemComp-A1J / 3-(5,7,7-trihydroxy-2,2,7-trioxo-6-oxa-2lambda~6~-thia-3-aza-7lambda~5~-phospha-5-boraheptan-1-yl)benzoic acid


Mass: 353.051 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13BNO9PS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 586 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ADC-7 (3mg/mL) in 25% w/v polyethylene glycol (PEG) 1500, 0.1 M succinate/ phosphate/ glycine

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0782 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 1.804→81.459 Å / Num. obs: 124952 / % possible obs: 99.4 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.1
Reflection shellResolution: 1.804→1.81 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1257 / CC1/2: 0.758 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U0T

4u0t


Resolution: 1.804→81.459 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.469 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23231 6269 5 %RANDOM
Rwork0.18284 ---
obs0.18526 118659 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20.97 Å2
2---1.67 Å20 Å2
3---0.35 Å2
Refinement stepCycle: 1 / Resolution: 1.804→81.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11104 0 88 586 11778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211531
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210444
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.97215724
X-RAY DIFFRACTIONr_angle_other_deg1.08324388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.19351439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.76825.711499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.061151906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.161523
X-RAY DIFFRACTIONr_chiral_restr0.1470.21741
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112786
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022173
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_it2.893.1675713
X-RAY DIFFRACTIONr_mcbond_other2.8893.1665712
X-RAY DIFFRACTIONr_mcangle_it3.6254.7327138
X-RAY DIFFRACTIONr_mcangle_other3.6264.7337139
X-RAY DIFFRACTIONr_scbond_it3.5563.5255818
X-RAY DIFFRACTIONr_scbond_other3.5553.5245813
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1065.1458571
X-RAY DIFFRACTIONr_long_range_B_refined6.21638.01312918
X-RAY DIFFRACTIONr_long_range_B_other6.20737.92712833
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.804→1.851 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 480 -
Rwork0.267 8749 -
obs--99.22 %

+
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