[English] 日本語
Yorodumi
- PDB-3bff: class A beta-lactamase SED-G238C complexed with faropenem -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bff
Titleclass A beta-lactamase SED-G238C complexed with faropenem
ComponentsClass A beta-lactamase Sed1
KeywordsHYDROLASE / BETA-LACTAMASE / CLASS A SED-G238C / FAROPENEM / ACYL-ENZYME
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 active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FPM / THIOCYANATE ION / Chem-SFR / Beta-lactamase
Similarity search - Component
Biological speciesCitrobacter sedlakii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPernot, L. / Petrella, S. / Sougakoff, W.
Citation
Journal: To be Published
Title: acyl-intermediate structures of the class A beta-lactamase SED-G238C
Authors: Pernot, L. / Petrella, S. / Sougakoff, W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and preliminary X-ray diffraction study of the class A beta-lactamase SED-1 and its mutant SED-G238C from Citrobacter sedlakii
Authors: Petrella, S. / Pernot, L. / Sougakoff, W.
History
DepositionNov 21, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 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
A: Class A beta-lactamase Sed1
B: Class A beta-lactamase Sed1
C: Class A beta-lactamase Sed1
D: Class A beta-lactamase Sed1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,16815
Polymers113,3214
Non-polymers1,84711
Water20,4111133
1
A: Class A beta-lactamase Sed1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6923
Polymers28,3301
Non-polymers3612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Class A beta-lactamase Sed1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8085
Polymers28,3301
Non-polymers4784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Class A beta-lactamase Sed1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9774
Polymers28,3301
Non-polymers6473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Class A beta-lactamase Sed1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6923
Polymers28,3301
Non-polymers3612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)187.116, 73.244, 103.504
Angle α, β, γ (deg.)90.00, 121.69, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Class A beta-lactamase Sed1


Mass: 28330.221 Da / Num. of mol.: 4 / Fragment: SED-G238C, UNP residues 34-295 / Mutation: G238C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter sedlakii (bacteria) / Strain: 2596 / Gene: bla-SED-1 / Plasmid: pET29a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q93PQ0, beta-lactamase
#2: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CNS
#3: Chemical
ChemComp-SFR / (2R)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-5-[(2R)-oxolan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylic acid / FAROPENEM, unbound, hydrolyzed form


Mass: 303.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H17NO6S / Comment: antibiotic*YM
#4: Chemical ChemComp-FPM / (5R,6S)-6-(1-hydroxyethyl)-7-oxo-3-[(2R)-oxolan-2-yl]-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid / Faropenem


Mass: 285.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15NO5S / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1133 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsSFR IS THE HYDROLYZED FORM OF FPM, BOUND TO THE PROTEIN VIA A COVALENT LINK WITH THE OG ATOM OF SER 70.
Sequence detailsTHIS COORDINATES IS USED NON-SEQUENTIAL RESIDUE NUMBERING. THREE NUMBERS, 58, 239, AND 253 WERE ...THIS COORDINATES IS USED NON-SEQUENTIAL RESIDUE NUMBERING. THREE NUMBERS, 58, 239, AND 253 WERE SIMPLY SKIPPED IN THE NUMBERING AND HAVE NOTHING TO DO WITH LACK OF ELECTRON DENSITY.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 35% PEG MME 2000, 200mM KSCN, 100mM sodium cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.984 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 16, 2002
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 90973 / Num. obs: 90973 / % possible obs: 97.2 % / Redundancy: 3.8 % / Rsym value: 0.083 / Net I/σ(I): 13.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 12685 / Rsym value: 0.279 / % possible all: 93.4

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
MOLREPphasing
CNS1.1refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BFD

3bfd


Resolution: 1.9→28.8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.205 3651 -RANDOM
Rwork0.18 ---
obs0.189 87314 96.7 %-
all-90965 --
Displacement parametersBiso mean: 12.05 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å20 Å2-1.01 Å2
2---1.21 Å20 Å2
3---3.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7948 0 113 1133 9194
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011
RfactorNum. reflection% reflection
Rfree0.269 580 -
Rwork0.231 14550 -
obs-14550 93.4 %

+
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