[English] 日本語
Yorodumi
- PDB-9il7: Crystal Structure of SME E166A in Complex with Ceftaroline Fosamil -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9il7
TitleCrystal Structure of SME E166A in Complex with Ceftaroline Fosamil
Componentsbeta-lactamase
KeywordsHYDROLASE / 5th Generation Cephalosporin / Carbapenemase / Complex
Function / homology
Function and homology information


transcription elongation-coupled chromatin remodeling / nucleosome binding / NADP binding / oxidoreductase activity / chromatin / DNA binding
Similarity search - Function
: / NADPH-dependent reductive aminase-like, C-terminal domain / : / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / IODIDE ION / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Oxidoreductase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDhankhar, K. / Hazra, S.
Funding support India, 2items
OrganizationGrant numberCountry
Board of Research in Nuclear Sciences (BRNS)54/14/03/2023-BRNS India
Indian Council of Medical ResearchEM/Dev/IG/20/0773/2023 India
CitationJournal: To Be Published
Title: Crystal Structure of SME E166A in Complex with Ceftaroline Fosamil
Authors: Dhankhar, K. / Hazra, S.
History
DepositionJun 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: beta-lactamase
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,08934
Polymers60,6912
Non-polymers3,39832
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.621, 51.076, 129.792
Angle α, β, γ (deg.)90, 90.123, 90
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein beta-lactamase / SME E166A


Mass: 30345.266 Da / Num. of mol.: 2 / Mutation: E166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: sme-2, blaSME-1, blaSME-4, blaSME1, SME12620_22 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q54488, beta-lactamase

-
Non-polymers , 8 types, 174 molecules

#2: Chemical ChemComp-A1L2O / (2~{R})-2-[(1~{R})-1-[[(2~{Z})-2-ethoxyimino-2-[5-(phosphonoamino)-1,2,4-thiadiazol-3-yl]ethanoyl]amino]-2-oxidanylidene-ethyl]-5-[[4-(1-methylpyridin-4-yl)-1,3-thiazol-2-yl]sulfanyl]-3,6-dihydro-2~{H}-1,3-thiazine-4-carboxylic acid


Mass: 687.709 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H24N8O8PS4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#7: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 4000, Lithium Chloride 0.2M

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→23.76 Å / Num. obs: 18330 / % possible obs: 99.3 % / Redundancy: 3.8 % / CC1/2: 0.993 / Rpim(I) all: 0.115 / Net I/σ(I): 7.5
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 1867 / CC1/2: 0.92 / Rpim(I) all: 0.167

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→21.741 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.888 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.182 / SU B: 0.004 / SU ML: 0 / Average fsc free: 0.9568 / Average fsc work: 0.9771 / Cross valid method: FREE R-VALUE / ESU R: 0.237 / ESU R Free: 0.324 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.2604 922 5.064 %0.2566
Rwork0.1904 17284 --
all0.194 ---
obs-18206 98.448 %-
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: 18.922 Å2
Baniso -1Baniso -2Baniso -3
1--1.019 Å2-0 Å20.204 Å2
2---0.425 Å2-0 Å2
3---1.444 Å2
Refinement stepCycle: LAST / Resolution: 2.4→21.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4092 0 184 142 4418
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
2.4-2.4620.352720.2412000.24512990.9270.96397.92150.229
2.462-2.5280.333560.23612600.2413320.930.96398.79880.224
2.528-2.60.321820.2311750.23612650.9390.96599.36760.22
2.6-2.6790.283670.22211540.22512300.9590.97199.26830.212
2.679-2.7660.275620.20911390.21212080.9510.97499.42050.199
2.766-2.8610.285630.20310880.20711530.9570.97699.82650.194
2.861-2.9670.264560.19410990.19711600.9560.97799.5690.184
2.967-3.0860.269530.1869840.19110390.9610.97899.80750.176
3.086-3.220.237370.17910170.18210550.9710.98199.90520.171
3.22-3.3740.249400.1619430.1649920.9560.98599.09270.154
3.374-3.5510.236390.1688920.1719480.9590.98598.20670.163
3.551-3.7610.253430.1848460.1888920.9790.98299.66370.178
3.761-4.0120.216410.1748190.1758750.9640.98498.28570.171
4.012-4.3210.261350.1697150.1737790.9620.98696.27730.167
4.321-4.7150.208420.1656600.1677370.9750.98595.2510.166
4.715-5.240.212380.1536190.1576810.9720.98896.47580.156
5.24-5.9930.241330.1935650.1966080.9760.98498.35530.195
5.993-7.2050.239270.2014830.2035160.9710.98398.83720.199
7.205-9.6720.281210.173730.1754110.9730.98995.86370.176
9.672-21.7410.164150.2162500.2132820.990.98493.97160.234

+
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