[English] 日本語
Yorodumi
- PDB-8rlk: Structure of the apo form of PIB-1 in an Orthorombic space group -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rlk
TitleStructure of the apo form of PIB-1 in an Orthorombic space group
ComponentsClass C beta-lactamase-related serine hydrolase
KeywordsHYDROLASE / Beta-lactamase / AmpC / PIB-1
Function / homology: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / hydrolase activity / Chem-MER / Serine hydrolase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMedrano, F.J. / Romero, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2020-113521RB-I00 Spain
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: A new type of Class C beta-lactamases defined by PIB-1. A metal-dependent carbapenem-hydrolyzing beta-lactamase, from Pseudomonas aeruginosa: Structural and functional analysis.
Authors: Medrano, F.J. / Hernando-Amado, S. / Martinez, J.L. / Romero, A.
History
DepositionJan 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 6, 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 C beta-lactamase-related serine hydrolase
B: Class C beta-lactamase-related serine hydrolase
C: Class C beta-lactamase-related serine hydrolase
D: Class C beta-lactamase-related serine hydrolase
E: Class C beta-lactamase-related serine hydrolase
F: Class C beta-lactamase-related serine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,49220
Polymers261,4196
Non-polymers2,07314
Water12,755708
1
A: Class C beta-lactamase-related serine hydrolase
B: Class C beta-lactamase-related serine hydrolase
C: Class C beta-lactamase-related serine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,20113
Polymers130,7103
Non-polymers1,49110
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-165 kcal/mol
Surface area41150 Å2
MethodPISA
2
D: Class C beta-lactamase-related serine hydrolase
hetero molecules

F: Class C beta-lactamase-related serine hydrolase
hetero molecules

E: Class C beta-lactamase-related serine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,2917
Polymers130,7103
Non-polymers5824
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
crystal symmetry operation3_455-x-1,y+1/2,-z+1/21
Buried area4890 Å2
ΔGint-133 kcal/mol
Surface area41930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.890, 101.452, 267.758
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein
Class C beta-lactamase-related serine hydrolase / Serine hydrolase


Mass: 43569.887 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: CAZ10_27720, DT376_01770, GUL26_24405 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1J0J3U4
#2: Chemical
ChemComp-MER / (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate buffer at pH 6.5 containing 20% PEG 1000 and 0.2 M MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.28368 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28368 Å / Relative weight: 1
ReflectionResolution: 2→47.44 Å / Num. obs: 145980 / % possible obs: 99.6 % / Redundancy: 10.64 % / Biso Wilson estimate: 36.16 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.08
Reflection shellResolution: 2→2.12 Å / Mean I/σ(I) obs: 10.7 / Num. unique obs: 23145 / CC1/2: 0.683 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIXdev_4746refinement
PHENIXdev_4746refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.44 Å / SU ML: 0.2813 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6761
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2353 2000 1.37 %
Rwork0.1913 143972 -
obs0.1919 145972 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.42 Å2
Refinement stepCycle: LAST / Resolution: 2→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18246 0 114 709 19069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007918810
X-RAY DIFFRACTIONf_angle_d1.017725518
X-RAY DIFFRACTIONf_chiral_restr0.05532652
X-RAY DIFFRACTIONf_plane_restr0.01023350
X-RAY DIFFRACTIONf_dihedral_angle_d6.99422638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.35481380.28999933X-RAY DIFFRACTION97.62
2.05-2.10.32531420.257210217X-RAY DIFFRACTION100
2.1-2.160.2751410.238710206X-RAY DIFFRACTION100
2.16-2.230.35731410.301110107X-RAY DIFFRACTION98.85
2.23-2.310.33111400.262310091X-RAY DIFFRACTION98.61
2.31-2.410.29081430.220110249X-RAY DIFFRACTION100
2.41-2.520.25941420.21410241X-RAY DIFFRACTION99.99
2.52-2.650.26461430.201510279X-RAY DIFFRACTION99.98
2.65-2.810.25171430.193110304X-RAY DIFFRACTION100
2.81-3.030.24851430.196710291X-RAY DIFFRACTION99.98
3.03-3.340.22991430.189910330X-RAY DIFFRACTION99.98
3.34-3.820.22191440.166510398X-RAY DIFFRACTION100
3.82-4.810.17861470.153310485X-RAY DIFFRACTION100
4.81-47.440.20781500.177310841X-RAY DIFFRACTION99.9

+
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