[English] 日本語
Yorodumi
- PDB-1kvl: X-ray Crystal Structure of AmpC S64G Mutant beta-Lactamase in Com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kvl
TitleX-ray Crystal Structure of AmpC S64G Mutant beta-Lactamase in Complex with Substrate and Product Forms of Cephalothin
ComponentsBeta-lactamase
KeywordsHYDROLASE / amide hydrolase / beta-lactamase / cephalothin / substrate-enzyme complex / product-enzyme 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
CEPHALOTHIN / Chem-KCP / PHOSPHATE ION / Chem-THN / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsBeadle, B.M. / Trehan, I. / Focia, P.J. / Shoichet, B.K.
CitationJournal: Structure / Year: 2002
Title: Structural milestones in the reaction pathway of an amide hydrolase: substrate, acyl, and product complexes of cephalothin with AmpC beta-lactamase.
Authors: Beadle, B.M. / Trehan, I. / Focia, P.J. / Shoichet, B.K.
History
DepositionJan 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4137
Polymers79,1162
Non-polymers1,2975
Water8,791488
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5015
Polymers39,5581
Non-polymers9434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9122
Polymers39,5581
Non-polymers3541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.619, 77.153, 98.066
Angle α, β, γ (deg.)90.00, 115.90, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase / Cephalosporinase


Mass: 39557.895 Da / Num. of mol.: 2 / Mutation: S64G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: K12 / Plasmid: pOGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase

-
Non-polymers , 5 types, 493 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-KCP / 2-[CARBOXY-(2-THIOPHEN-2-YL-ACETYLAMINO)-METHYL]-5-METHYL-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID / HYDROLYZED CEPHALOTHIN


Mass: 356.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N2O5S2
#4: Chemical ChemComp-CLS / CEPHALOTHIN / 3-ACETOXYMETHYL-8-OXO-7-(2-THIOPHEN-2-YL-ACETYLAMINO)-5-THIA-1-AZA-BICYCLO[4.2.0]OCT-2-ENE-2-CARBOXYLIC ACID


Mass: 396.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16N2O6S2 / Comment: antibiotic*YM
#5: Chemical ChemComp-THN / 2-[CARBOXY-(2-THIOPHEN-2-YL-ACETYLAMINO)-METHYL]-5-METHYLENE-5,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID / HYDROLYZED CEPHALOTHIN


Mass: 354.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14N2O5S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.79 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.7 M potassium phosphate; the crystal was then soaked in saturated cephalothin in crystallizing buffer for 3 hours, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃
Components of the solutions
*PLUS
Conc.: 1.7 M / Common name: potassium phosphate / Details: pH8.7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 11, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→20 Å / Num. obs: 108082 / % possible obs: 90.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 28.2
Reflection shellResolution: 1.53→1.57 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.14 / % possible all: 95.5
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 385475
Reflection shell
*PLUS
% possible obs: 95.5 % / Rmerge(I) obs: 0.4

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C3B

1c3b


Resolution: 1.53→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.22 2220 Random
Rwork0.195 --
all-108082 -
obs-89700 -
Solvent computationksol: 0.383662 e/Å3
Displacement parametersBiso mean: 54.1656 Å2
Baniso -1Baniso -2Baniso -3
1--3.573 Å20 Å2-4.646 Å2
2--2.884 Å20 Å2
3---0.689 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.53→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5553 0 105 488 6146
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_mcbond_it1.2631.5
X-RAY DIFFRACTIONc_scbond_it2.1022
X-RAY DIFFRACTIONc_mcangle_it1.8352
X-RAY DIFFRACTIONc_scangle_it3.0822.5
LS refinement shellResolution: 1.53→1.58 Å
RfactorNum. reflection
Rfree0.223 184
Rwork0.213 -
obs-6960
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cephalothin.paramcephalothin.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 2.5 % / Rfactor obs: 0.195 / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Lowest resolution: 1.57 Å

+
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