[English] 日本語
Yorodumi
- PDB-9jnd: Crystal Structure of SME-1 E166A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9jnd
TitleCrystal Structure of SME-1 E166A mutant
Componentsbeta-lactamase
KeywordsHYDROLASE / Deacylation deficient mutant / Carbapenemase / AMR
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Beta-lactamase SME-1
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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-1 E166A mutant
Authors: Dhankhar, K. / Hazra, S.
History
DepositionSep 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 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)61,1338
Polymers60,6912
Non-polymers4426
Water3,243180
1
A: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5392
Polymers30,3451
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11190 Å2
MethodPISA
2
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5936
Polymers30,3451
Non-polymers2485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-13 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.708, 51.828, 77.192
Angle α, β, γ (deg.)90, 114.235, 90
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ASP / End label comp-ID: ASP / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 267 / Label seq-ID: 3 - 269

Dom-ID
1
2

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

-
Components

#1: Protein beta-lactamase / SME E166A


Mass: 30345.266 Da / Num. of mol.: 2
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
#2: 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
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.22 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 4000, 0.2M Lithium Chloride

-
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: Jul 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→25.884 Å / Num. obs: 23268 / % possible obs: 99.9 % / Redundancy: 8.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.058 / Rrim(I) all: 0.12 / Net I/σ(I): 15.4
Reflection shell

Diffraction-ID: 1 / Redundancy: 6 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.61-25.870.0354590.9990.020.04
2.3-2.390.38224490.8930.2580.464

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata collection
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→25.884 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.908 / SU B: 16.959 / SU ML: 0.178 / Cross valid method: FREE R-VALUE / ESU R Free: 0.246 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2371 1113 4.786 %
Rwork0.174 22141 -
all0.177 --
obs-23254 99.88 %
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: 22.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.733 Å20 Å2-0.745 Å2
2---0.986 Å20 Å2
3---1.701 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4112 0 24 180 4316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124234
X-RAY DIFFRACTIONr_angle_refined_deg1.8271.8185706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6465540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.422532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.23310756
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.07610186
X-RAY DIFFRACTIONr_chiral_restr0.1370.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023190
X-RAY DIFFRACTIONr_nbd_refined0.2150.21932
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22897
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2242
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3180.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1220.25
X-RAY DIFFRACTIONr_mcbond_it1.6771.1262142
X-RAY DIFFRACTIONr_mcangle_it2.7812.0242676
X-RAY DIFFRACTIONr_scbond_it2.1681.1972092
X-RAY DIFFRACTIONr_scangle_it3.4052.1683026
X-RAY DIFFRACTIONr_lrange_it8.71712.1066477
X-RAY DIFFRACTIONr_rigid_bond_restr2.53634234
X-RAY DIFFRACTIONr_ncsr_local_group_10.0620.058913
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.061740.05009
12AX-RAY DIFFRACTIONLocal ncs0.061740.05009
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
2.3-2.3590.284830.20416280.20717110.9360.9711000.183
2.359-2.4230.292950.19415340.20116290.9430.9731000.175
2.423-2.4930.236710.19315490.19516200.9650.9751000.171
2.493-2.5690.279700.214780.20315480.9430.9761000.178
2.569-2.6520.256790.18914370.19215160.9580.9791000.167
2.652-2.7440.284610.18814410.19215020.9570.9771000.169
2.744-2.8470.295630.17913290.18413930.940.98199.92820.157
2.847-2.9620.267620.20412910.20713530.9540.9731000.183
2.962-3.0910.251670.19312570.19613250.9580.97699.92450.172
3.091-3.240.252610.19311950.19712560.9550.9771000.18
3.24-3.4120.205700.17411200.17511900.9740.9861000.168
3.412-3.6150.226730.17210560.17511290.9750.9861000.165
3.615-3.860.221720.16210150.16510880.9710.98799.90810.156
3.86-4.1610.205230.1539650.1549890.9780.98799.89890.151
4.161-4.5460.19250.1419020.1429270.9780.9891000.141
4.546-5.0640.224330.1318090.1348420.9780.9911000.133
5.064-5.810.187320.1497230.1517550.9810.9881000.146
5.81-7.0280.274190.1876200.196390.9590.9831000.179
7.028-9.5920.136290.1434880.1425170.990.9911000.145
9.592-25.8840.235250.1693040.1743330.9640.98598.79880.173
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)
11.4577-0.12220.20671.7670.78791.68160.09320.0164-0.00630.0772-0.0992-0.26720.0065-0.01050.0060.0256-0.0316-0.0280.05690.03750.060813.35170.0968.0268
22.1593-0.13570.29151.7720.63771.5523-0.0252-0.1032-0.05340.12980.0929-0.15590.03840.0401-0.06770.01370.003-0.02240.01440.00730.0482-1.73371.663241.8085
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