[English] 日本語
Yorodumi
- PDB-6ua1: Crystal Structure of the metallo-beta-lactamase L1 from Stenotrop... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ua1
TitleCrystal Structure of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the no-metal bound form
ComponentsPutative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
KeywordsHYDROLASE / lactam antibiotics / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the no-metal bound form.
Authors: Kim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3062
Polymers29,2441
Non-polymers621
Water2,270126
1
A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules

A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules

A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules

A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2248
Polymers116,9764
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area9190 Å2
ΔGint-49 kcal/mol
Surface area39920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.467, 104.467, 99.035
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11A-523-

HOH

-
Components

#1: Protein Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)


Mass: 29243.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: Smlt2667 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): gold / References: UniProt: B2FTM1, beta-lactamase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M sodium malonate pH 7.0, 20 % w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 29676 / % possible obs: 98.7 % / Redundancy: 14.6 % / Biso Wilson estimate: 35.47 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 31
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 0.67 / Num. unique obs: 1215 / CC1/2: 0.552 / % possible all: 83.2

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 6U0Y

6u0y


Resolution: 1.8→41.15 Å / SU ML: 0.2749 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 28.7856
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 1511 5.13 %random
Rwork0.191 ---
obs0.1927 29445 97.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.63 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 0 126 2129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552092
X-RAY DIFFRACTIONf_angle_d0.77482859
X-RAY DIFFRACTIONf_chiral_restr0.0512317
X-RAY DIFFRACTIONf_plane_restr0.0057380
X-RAY DIFFRACTIONf_dihedral_angle_d13.77071243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.39461070.39592066X-RAY DIFFRACTION81.54
1.86-1.920.43171410.34182481X-RAY DIFFRACTION97.91
1.92-20.31371310.292545X-RAY DIFFRACTION99.7
2-2.090.28441380.24562546X-RAY DIFFRACTION99.52
2.09-2.20.26661370.22462551X-RAY DIFFRACTION99.93
2.2-2.340.25221390.20672554X-RAY DIFFRACTION99.93
2.34-2.520.26011420.19892582X-RAY DIFFRACTION99.85
2.52-2.780.26631300.21552595X-RAY DIFFRACTION99.85
2.78-3.180.2351420.21742610X-RAY DIFFRACTION99.78
3.18-40.22081470.17462634X-RAY DIFFRACTION99.43
4-41.150.16061570.1472770X-RAY DIFFRACTION98.85
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)
10.08347037177030.04108771587730.01036543724970.02031530557720.025986893631-0.00602370414958-0.334815284829-0.483146395877-0.229368356303-0.006736022140260.1892786572230.2059121085910.0634166359532-0.353382244426-6.39881956638E-50.7149322947490.007108322039940.06043620110890.476234408208-0.02215623623280.62006522266924.194907062-5.593042809391.83561597195
20.285744508847-0.302875657973-0.2641117092910.2817401041190.1833727648140.362594394425-0.05588115305680.06026574250550.05473711750470.053169360749-0.02571504693150.131874100066-0.16544556874-0.230509223403-0.0001140785799250.4936122904180.0382166309775-0.04640650790080.294662905725-0.01589152926560.40293385596435.555544199821.26897431049.61941393232
30.185124355445-0.287749704395-0.1168429901770.3213491736480.05076957535850.178853532249-0.04722312203150.122300368349-0.0486375510939-0.189204394947-0.0590381924113-0.0754500435733-0.194964966274-0.04155466674320.0002702111398780.4849846380130.0237379310775-0.02502277754490.320904559472-0.01138011375710.32365590553142.989908793415.73108998914.76365680866
40.326197229249-0.424314391440.09078096250610.468909293574-0.1501974723110.2031563530950.03182592571270.0184446991241-0.08852685304640.151799002487-0.0755229650030.09733463382920.0308457012069-0.09572700114752.53571533539E-50.437029120550.04126070705130.01239806845570.31290590227-0.02645062729470.34874024516645.20401455972.671782040179.69470497432
51.00314811037-0.4790206087870.1347293905120.614085857014-0.6229946628690.637634590973-0.186067243735-0.1244394077350.06111532484970.4101497003770.0525447913154-0.0125754773149-0.02366836811610.0408335044139-0.0001369322388220.4931551949340.020370464419-0.01679246134430.250511485992-0.02920631835280.32624505713943.514404911611.785212588421.2443980526
60.3328974979280.146834354131-0.1162417391870.0808158994833-0.03362977982180.140521579891-0.0551861871069-0.2524873396090.01394998748620.68446340914-0.153771794677-0.122934793978-0.1678613562580.07001015425990.0002068784902870.5628647355180.0810349886030.00188732154650.354268491760.005297416725530.35970651801942.26455902368.0348409374928.1682247035
70.07062954681430.052072839118-0.07443334980010.0266600944319-0.05969610511020.0808764576065-0.1471078753220.04645357258420.05887925070160.4512078284040.3671590406140.180437606827-0.0429493754844-0.7434694315690.001677029839720.5390550605670.1351723032310.03566307071080.459973990816-0.02347032585150.38376481360929.607981851219.849592525422.8760402566
80.298793573638-0.3624456738520.1753864743940.434998634329-0.1491121273150.0805919515063-0.223641771465-0.04777845110850.01442339672320.2465604445670.4496502631610.453043705501-0.233676810567-0.9800749436970.04728770900990.5674052648060.0978164791010.1646823159880.530633854062-0.001102455550910.4056008321333.0527731110.97512851447831.1315329587
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 90 )
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 125 )
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 164 )
5X-RAY DIFFRACTION5chain 'A' and (resid 165 through 222 )
6X-RAY DIFFRACTION6chain 'A' and (resid 223 through 244 )
7X-RAY DIFFRACTION7chain 'A' and (resid 245 through 266 )
8X-RAY DIFFRACTION8chain 'A' and (resid 267 through 288 )

+
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://pdbjlvh1.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