[English] 日本語
Yorodumi
- PDB-6b69: Beta-Lactamase, 500ms timepoint, mixed, shards crystal form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b69
TitleBeta-Lactamase, 500ms timepoint, mixed, shards crystal form
ComponentsBeta-lactamase
KeywordsHYDROLASE/ANTIBIOTIC / Beta-Lactamase / ANTIBIOTIC / HYDROLASE-ANTIBIOTIC complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane
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
Ceftriaxone / Chem-CUG / Chem-FZS / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / Resolution: 2.2 Å
AuthorsPandey, S. / Schmidt, M.
CitationJournal: BMC Biol. / Year: 2018
Title: Enzyme intermediates captured "on the fly" by mix-and-inject serial crystallography.
Authors: Olmos, J.L. / Pandey, S. / Martin-Garcia, J.M. / Calvey, G. / Katz, A. / Knoska, J. / Kupitz, C. / Hunter, M.S. / Liang, M. / Oberthuer, D. / Yefanov, O. / Wiedorn, M. / Heyman, M. / Holl, M. ...Authors: Olmos, J.L. / Pandey, S. / Martin-Garcia, J.M. / Calvey, G. / Katz, A. / Knoska, J. / Kupitz, C. / Hunter, M.S. / Liang, M. / Oberthuer, D. / Yefanov, O. / Wiedorn, M. / Heyman, M. / Holl, M. / Pande, K. / Barty, A. / Miller, M.D. / Stern, S. / Roy-Chowdhury, S. / Coe, J. / Nagaratnam, N. / Zook, J. / Verburgt, J. / Norwood, T. / Poudyal, I. / Xu, D. / Koglin, J. / Seaberg, M.H. / Zhao, Y. / Bajt, S. / Grant, T. / Mariani, V. / Nelson, G. / Subramanian, G. / Bae, E. / Fromme, R. / Fung, R. / Schwander, P. / Frank, M. / White, T.A. / Weierstall, U. / Zatsepin, N. / Spence, J. / Fromme, P. / Chapman, H.N. / Pollack, L. / Tremblay, L. / Ourmazd, A. / Phillips, G.N. / Schmidt, M.
History
DepositionOct 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,84312
Polymers113,6034
Non-polymers3,2398
Water7,044391
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.860, 96.310, 113.560
Angle α, β, γ (deg.)90.00, 109.98, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-lactamase / Ambler class A beta-lactamase


Mass: 28400.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: blaC, blaA, Rv2068c, MTCY49.07c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WKD3, beta-lactamase

-
Non-polymers , 5 types, 399 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-9F2 / Ceftriaxone


Mass: 554.580 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H18N8O7S3
#4: Chemical ChemComp-CUG / (2R)-2-[(S)-{[(2E)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino}(carboxy)methyl]-5-(hydroxymethyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid


Mass: 431.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17N5O7S2
#5: Chemical ChemComp-FZS / (2R)-2-[(1S)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino}-2-hydroxyethyl]-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / Ceftriaxone open, bound form


Mass: 399.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17N5O5S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.68 %
Crystal growTemperature: 300 K / Method: microbatch / Details: Ammonium Phosphate

-
Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Sep 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 2.2→20.25 Å / Num. obs: 72804 / % possible obs: 100 % / Redundancy: 1363.04 % / Net I/σ(I): 8.3
Reflection shellResolution: 2.2→2.23 Å / Redundancy: 81.3 % / Mean I/σ(I) obs: 0.9 / CC1/2: 0.31 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementResolution: 2.2→20.253 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2628 3550 4.88 %
Rwork0.2413 --
obs0.2424 72804 89.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→20.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7952 0 207 391 8550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038329
X-RAY DIFFRACTIONf_angle_d1.41711383
X-RAY DIFFRACTIONf_dihedral_angle_d18.9554952
X-RAY DIFFRACTIONf_chiral_restr0.0451288
X-RAY DIFFRACTIONf_plane_restr0.0041516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.23010.34841320.33762296X-RAY DIFFRACTION75
2.2301-2.26190.37761040.33082256X-RAY DIFFRACTION73
2.2619-2.29560.37381390.33532332X-RAY DIFFRACTION77
2.2956-2.33150.38611230.34082474X-RAY DIFFRACTION80
2.3315-2.36960.38571350.31062485X-RAY DIFFRACTION82
2.3696-2.41040.3461260.29072541X-RAY DIFFRACTION83
2.4104-2.45420.31621350.28452543X-RAY DIFFRACTION83
2.4542-2.50130.36071370.28052596X-RAY DIFFRACTION85
2.5013-2.55230.36591460.2822609X-RAY DIFFRACTION85
2.5523-2.60770.3551230.29342586X-RAY DIFFRACTION83
2.6077-2.66820.34641180.28662450X-RAY DIFFRACTION80
2.6682-2.73480.34081380.26012456X-RAY DIFFRACTION81
2.7348-2.80850.29641510.25422775X-RAY DIFFRACTION90
2.8085-2.89090.28551330.25012924X-RAY DIFFRACTION95
2.8909-2.9840.28281630.25153008X-RAY DIFFRACTION98
2.984-3.09020.27851540.23683074X-RAY DIFFRACTION100
3.0902-3.21350.25651470.22333069X-RAY DIFFRACTION100
3.2135-3.35910.26231500.22713087X-RAY DIFFRACTION100
3.3591-3.53540.25411590.2153085X-RAY DIFFRACTION100
3.5354-3.75550.22511420.2133089X-RAY DIFFRACTION100
3.7555-4.04340.22461180.20943117X-RAY DIFFRACTION99
4.0434-4.44640.23061940.20683043X-RAY DIFFRACTION100
4.4464-5.08090.18131800.20093078X-RAY DIFFRACTION100
5.0809-6.36820.25711580.24023118X-RAY DIFFRACTION100
6.3682-20.25370.22291450.25473163X-RAY DIFFRACTION99

+
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