[English] 日本語
Yorodumi
- PDB-8cf3: Crystal structure of S. aureus BlaR1 sensor domain in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cf3
TitleCrystal structure of S. aureus BlaR1 sensor domain in complex with cefepime
ComponentsRegulatory protein BlaR1
KeywordsSIGNALING PROTEIN / Antibiotic resistance / Beta-lactam sensor of Staphylococcus aureus / MRSA
Function / homology
Function and homology information


penicillin binding / plasma membrane
Similarity search - Function
: / Peptidase M56 / BlaR1 peptidase M56 / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
: / Regulatory protein BlaR1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsMiguel-Ruano, V. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU2017-90030-P Spain
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Restoring susceptibility to beta-lactam antibiotics in methicillin-resistant Staphylococcus aureus.
Authors: Nguyen, V.T. / Birhanu, B.T. / Miguel-Ruano, V. / Kim, C. / Batuecas, M. / Yang, J. / El-Araby, A.M. / Jimenez-Faraco, E. / Schroeder, V.A. / Alba, A. / Rana, N. / Sader, S. / Thomas, C.A. / ...Authors: Nguyen, V.T. / Birhanu, B.T. / Miguel-Ruano, V. / Kim, C. / Batuecas, M. / Yang, J. / El-Araby, A.M. / Jimenez-Faraco, E. / Schroeder, V.A. / Alba, A. / Rana, N. / Sader, S. / Thomas, C.A. / Feltzer, R. / Lee, M. / Fisher, J.F. / Hermoso, J.A. / Chang, M. / Mobashery, S.
History
DepositionFeb 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Regulatory protein BlaR1
E: Regulatory protein BlaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8854
Polymers58,9142
Non-polymers9712
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-3 kcal/mol
Surface area23210 Å2
Unit cell
Length a, b, c (Å)46.819, 109.470, 50.297
Angle α, β, γ (deg.)90.000, 103.657, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 333 - 583 / Label seq-ID: 1 - 251

Dom-IDAuth asym-IDLabel asym-ID
1CA
2EB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein Regulatory protein BlaR1


Mass: 29457.121 Da / Num. of mol.: 2 / Mutation: Triple mutant K369A K370A K372A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: blaR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18357
#2: Chemical ChemComp-UJ9 / Cefepime (open) / (2R,5S)-2-[(1R)-1-[[(2Z)-2-(2-azanyl-1,3-thiazol-4-yl)-2-methoxyimino-ethanoyl]amino]-2-oxidanyl-ethyl]-5-[(1-methylpyrrolidin-1-ium-1-yl)methyl]-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / Cefepimum (reacted)


Mass: 485.601 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H29N6O5S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.25
Details: Soidum Cacodylate 0.085M pH 5.5 + PEG 8K 27% + Glycerol 15%

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.0064 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0064 Å / Relative weight: 1
ReflectionResolution: 2.153→45.537 Å / Num. obs: 17584 / % possible obs: 82.55 % / Redundancy: 6.05 % / CC1/2: 0.9969 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.057 / Rrim(I) all: 0.142 / Net I/σ(I): 9.186
Reflection shellResolution: 2.153→2.345 Å / Rmerge(I) obs: 1.772 / Num. unique obs: 880 / CC1/2: 0.3028 / Rpim(I) all: 0.865

-
Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→45.537 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.888 / SU B: 35.026 / SU ML: 0.356 / Cross valid method: FREE R-VALUE / ESU R Free: 0.391
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.27 778 5.148 %
Rwork0.2165 14334 -
all0.219 --
obs-15112 90.605 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 54.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.294 Å20 Å23.124 Å2
2--3.39 Å20 Å2
3----4.127 Å2
Refinement stepCycle: LAST / Resolution: 2.52→45.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4140 0 76 59 4275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0124326
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163950
X-RAY DIFFRACTIONr_angle_refined_deg0.9171.6725832
X-RAY DIFFRACTIONr_angle_other_deg0.3381.6049112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1135500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.438510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56710778
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.8510220
X-RAY DIFFRACTIONr_chiral_restr0.0790.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021050
X-RAY DIFFRACTIONr_nbd_refined0.1920.2866
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.23670
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22089
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22154
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2134
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1290.210
X-RAY DIFFRACTIONr_nbd_other0.2370.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2020.22
X-RAY DIFFRACTIONr_mcbond_it1.1132.5172006
X-RAY DIFFRACTIONr_mcbond_other1.1132.5172006
X-RAY DIFFRACTIONr_mcangle_it2.0124.5182504
X-RAY DIFFRACTIONr_mcangle_other2.0124.5192505
X-RAY DIFFRACTIONr_scbond_it0.912.6022320
X-RAY DIFFRACTIONr_scbond_other0.912.6032321
X-RAY DIFFRACTIONr_scangle_it1.6794.7443328
X-RAY DIFFRACTIONr_scangle_other1.6794.7463329
X-RAY DIFFRACTIONr_lrange_it3.50724.5364997
X-RAY DIFFRACTIONr_lrange_other3.48324.5194986
X-RAY DIFFRACTIONr_ncsr_local_group_10.080.059079
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11CX-RAY DIFFRACTIONLocal ncs0.079540.05011
12EX-RAY DIFFRACTIONLocal ncs0.079540.05011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.52-2.5850.339470.2796880.28212250.9470.958600.241
2.585-2.6560.275420.2657820.26611900.9390.96469.24370.218
2.656-2.7330.292390.2998700.29811680.9450.94977.82530.258
2.733-2.8160.385560.2768730.28311070.9160.9683.92050.226
2.816-2.9080.297580.2739520.27411160.9490.96390.50180.214
2.908-3.010.399570.2679320.27410420.9080.96594.91360.213
3.01-3.1230.334460.2559890.25810440.9350.96699.13790.207
3.123-3.250.28550.2548940.2569610.9530.96498.75130.209
3.25-3.3940.33520.2228900.2289560.9340.97398.53560.188
3.394-3.5580.218400.228590.229100.9770.97798.79120.184
3.558-3.750.236380.2087990.2098470.9580.97898.81940.183
3.75-3.9750.198420.1927700.1938170.9850.9899.3880.175
3.975-4.2470.175360.1657370.1667820.9780.98598.84910.158
4.247-4.5840.273320.1736750.1777140.9610.98399.01960.169
4.584-5.0170.254340.1746090.1796530.9640.98398.46860.172
5.017-5.6010.277230.2035680.2065950.9710.97899.32770.197
5.601-6.4510.312190.2495050.2525270.9420.9799.43070.243
6.451-7.8610.285260.2544230.2564530.9570.96599.1170.25
7.861-10.9550.267190.1453310.1523540.960.98698.87010.151
10.955-45.5370.239170.2181840.222120.9780.97494.81130.228
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)
12.57140.14870.98921.3421-0.27951.72530.0476-0.03610.164-0.0522-0.0555-0.05010.0076-0.1020.00790.304-0.0146-0.24160.0167-0.01360.467820.97937.2374.3098
21.4801-0.53020.73691.1046-0.29882.6087-0.0596-0.2303-0.1028-0.14470.0403-0.04180.1156-0.09340.01930.34370.0232-0.26220.0380.01540.437535.686-18.367525.3951
Refinement TLS groupSelection: ALL

+
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