[English] 日本語
Yorodumi
- PDB-6uah: Crystal Structure of the Metallo-beta-Lactamase L1 from Stenotrop... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uah
TitleCrystal Structure of the Metallo-beta-Lactamase L1 from Stenotrophomonas maltophilia in the Complex with Hydrolyzed Meropenem
ComponentsPutative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
KeywordsHYDROLASE / lactam antibiotics / carbapenem / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


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 superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LMP / TRIETHYLENE GLYCOL / beta-lactamase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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 Complex with Hydrolyzed Meropenem
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 ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Nov 20, 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: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9886
Polymers29,2441
Non-polymers7455
Water2,666148
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)119,95424
Polymers116,9764
Non-polymers2,97820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area11750 Å2
ΔGint-3 kcal/mol
Surface area37620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.410, 104.410, 98.849
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-413-

HOH

21A-472-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#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

-
Non-polymers , 5 types, 153 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-LMP / (2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-(dimethylcarbamoy l)pyrrolidin-3-yl]sulfanyl-3-methyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid / Hydrolyzed Meropenem


Mass: 401.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M tatrate, 20 % (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 22788 / % possible obs: 100 % / Redundancy: 20.5 % / Biso Wilson estimate: 29.13 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.11 / Net I/σ(I): 41
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 17.6 % / Rmerge(I) obs: 0.974 / Mean I/σ(I) obs: 4.38 / Num. unique obs: 1101 / CC1/2: 0.929 / % possible all: 100

-
Processing

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

6u0y


Resolution: 1.98→35.89 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.6
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 1132 5.13 %RANDOM
Rwork0.1729 ---
obs0.1745 22055 96.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.9 Å2
Refinement stepCycle: LAST / Resolution: 1.98→35.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1990 0 43 148 2181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062126
X-RAY DIFFRACTIONf_angle_d0.7932902
X-RAY DIFFRACTIONf_chiral_restr0.049321
X-RAY DIFFRACTIONf_plane_restr0.005381
X-RAY DIFFRACTIONf_dihedral_angle_d12.6711259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.070.25571340.19722583X-RAY DIFFRACTION98
2.07-2.180.24721480.18792610X-RAY DIFFRACTION98
2.18-2.310.22771320.19072561X-RAY DIFFRACTION97
2.31-2.490.26331280.1892559X-RAY DIFFRACTION96
2.49-2.740.26161430.19542556X-RAY DIFFRACTION96
2.74-3.140.22271370.18552576X-RAY DIFFRACTION96
3.14-3.950.17031480.16012633X-RAY DIFFRACTION97
3.95-35.890.17531620.15622845X-RAY DIFFRACTION98
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)
10.953700006-0.5934000015-0.00970000035.1554999352-1.83879995352.907200098-0.15639999510.03170000020.29969999190.1204999983-0.1772000045-0.7944999933-0.40209999680.34909999370.17380000650.3661000133-0.0121999998-0.03009999920.30860000850.05200000110.4034999907-29.7474002838-13.42850017559.5032997131
22.5811998844-0.6565999985-0.47760000823.3368999958-0.45129999523.24140000340.04170000180.1305000037-0.2931999862-0.1643999964-0.11240000280.09200000020.30160000920.15700000520.10750000180.27759999040.01510000040.01689999920.2011999935-0.01620000040.2436999977-40.8554000854-21.82489967355.8380999565
31.5104999542-0.4988000095-0.04230000080.95410001280.50249999761.3407000303-0.00230000010.0399000011-0.08070000260.0504000001-0.09279999880.07000000030.02610000040.01799999920.10230000320.18960000570.0077999998-0.00270000010.13289999960.01229999960.1634999961-44.6337013245-11.774800300613.5094003677
43.7857999802-2.0174000263-0.32220000037.33120012280.26930001381.5767999887-0.0571999997-0.16169999540.3210999966-0.02470000090.1445000023-0.122299999-0.15039999780.1142999977-0.07580000160.2433999926-0.0287999995-0.04239999880.21289999780.00440.2021999955-38.60179901125.082699775721.7077007294
51.6040999889-0.2937000096-0.03409999986.98190021510.31589999792.0388998985-0.1704999954-0.2001000047-0.07159999760.60049998760.09499999880.21860000490.0621999986-0.10230000320.07970000060.25600001220.0260000005-0.02030000090.19539999960.00650000010.1713999957-42.5340995789-7.820000171728.179599762
62.0164999962-0.5856999755-0.34599998592.99629998210.23870000242.8875000477-0.00660.0348000005-0.08560000360.15999999640.2214999944-0.34180000420.35240000490.3370999992-0.12720000740.25600001220.0421999991-0.02710000050.27459999920.00880.2572999895-29.552400589-20.00219917322.8404998779
73.8022000791.26600003240.84850001342.10739994050.92949998383.3787000179-0.0834999979-0.19789999720.22550000250.4695999920.0790999979-0.1758999974-0.15360000730.32319998740.03170000020.32980000970.0430000015-0.09390000250.31049999590.00290.2657999992-32.9161987305-0.872300028830.8342990875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 61 )
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 102 )
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 204 )
4X-RAY DIFFRACTION4chain 'A' and (resid 205 through 222 )
5X-RAY DIFFRACTION5chain 'A' and (resid 223 through 244 )
6X-RAY DIFFRACTION6chain 'A' and (resid 245 through 266 )
7X-RAY DIFFRACTION7chain '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://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