[English] 日本語
Yorodumi
- PDB-5qb4: OXA-48 IN COMPLEX WITH SUBSTRATE IMIPENEM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5qb4
TitleOXA-48 IN COMPLEX WITH SUBSTRATE IMIPENEM
ComponentsBeta-lactamase
KeywordsHYDROLASE / Oxacillinase / Inhibitor / Complex / OXA / Antibiotic resistance / beta-lactamase / fragment
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase / beta-lactamase activity / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-IM2 / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLund, B.A. / Leiros, H.K.S.
CitationJournal: Eur J Med Chem / Year: 2018
Title: A focused fragment library targeting the antibiotic resistance enzyme - Oxacillinase-48: Synthesis, structural evaluation and inhibitor design.
Authors: Akhter, S. / Lund, B.A. / Ismael, A. / Langer, M. / Isaksson, J. / Christopeit, T. / Leiros, H.S. / Bayer, A.
History
DepositionJul 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Structure summary / Category: pdbx_deposit_group
Item: _pdbx_deposit_group.group_title / _pdbx_deposit_group.group_type
Revision 1.2Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Nov 17, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_deposit_group / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_deposit_group.group_description / _pdbx_entity_nonpoly.name
Revision 1.4Nov 15, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
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)114,24611
Polymers112,9084
Non-polymers1,3387
Water14,052780
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5282
Polymers28,2271
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5282
Polymers28,2271
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6264
Polymers28,2271
Non-polymers3993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5643
Polymers28,2271
Non-polymers3372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.790, 107.500, 124.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 24 through 39 or resid 41...
21(chain B and (resid 24 through 39 or resid 41...
31(chain C and (resid 24 through 39 or resid 41...
41(chain D and (resid 24 through 39 or resid 41...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULYSLYS(chain A and (resid 24 through 39 or resid 41...AA24 - 392 - 17
12GLNGLNLEULEU(chain A and (resid 24 through 39 or resid 41...AA41 - 13919 - 117
13ALAALAASNASN(chain A and (resid 24 through 39 or resid 41...AA141 - 231119 - 209
14TRPTRPPROPRO(chain A and (resid 24 through 39 or resid 41...AA233 - 265211 - 243
21GLUGLULYSLYS(chain B and (resid 24 through 39 or resid 41...BB24 - 392 - 17
22GLNGLNLEULEU(chain B and (resid 24 through 39 or resid 41...BB41 - 13919 - 117
23ALAALAASNASN(chain B and (resid 24 through 39 or resid 41...BB141 - 231119 - 209
24TRPTRPPROPRO(chain B and (resid 24 through 39 or resid 41...BB233 - 265211 - 243
31GLUGLULYSLYS(chain C and (resid 24 through 39 or resid 41...CC24 - 392 - 17
32GLNGLNLEULEU(chain C and (resid 24 through 39 or resid 41...CC41 - 13919 - 117
33ALAALAASNASN(chain C and (resid 24 through 39 or resid 41...CC141 - 231119 - 209
34TRPTRPPROPRO(chain C and (resid 24 through 39 or resid 41...CC233 - 265211 - 243
41GLUGLULYSLYS(chain D and (resid 24 through 39 or resid 41...DD24 - 392 - 17
42GLNGLNLEULEU(chain D and (resid 24 through 39 or resid 41...DD41 - 13919 - 117
43ALAALAASNASN(chain D and (resid 24 through 39 or resid 41...DD141 - 231119 - 209
44TRPTRPPROPRO(chain D and (resid 24 through 39 or resid 41...DD233 - 265211 - 243

-
Components

#1: Protein
Beta-lactamase


Mass: 28226.951 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical
ChemComp-IM2 / (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form


Mass: 301.362 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N3O4S / Comment: antibiotic*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 780 / 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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 8-11% PEG 8000 and 4-8% 1-butanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976254 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.95→43.13 Å / % possible obs: 95.55 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.1019 / Rrim(I) all: 0.11 / Net I/σ(I): 9.13
Reflection shellResolution: 1.95→2.02 Å / % possible obs: 93.89 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.6324 / Num. unique obs: 36743 / Rrim(I) all: 0.71 / Net I/σ(I) obs: 2.24

-
Processing

Software
NameVersionClassificationNB
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY: 5dtk

5dtk


Resolution: 1.95→43.13 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2197 4100 -
Rwork0.1848 --
obs-83386 95.55 %
Refinement stepCycle: final / Resolution: 1.95→43.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 160 780 8872
Biso mean--65.86 43.08 -
Num. residues----968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088257
X-RAY DIFFRACTIONf_angle_d0.83511172
X-RAY DIFFRACTIONf_chiral_restr0.0531175
X-RAY DIFFRACTIONf_plane_restr0.0051451
X-RAY DIFFRACTIONf_dihedral_angle_d18.3834863
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6123X-RAY DIFFRACTION4.693TORSIONAL
12B6123X-RAY DIFFRACTION4.693TORSIONAL
13C6123X-RAY DIFFRACTION4.693TORSIONAL
14D6123X-RAY DIFFRACTION4.693TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.9730.33961290.3062388251785
1.973-1.9970.28241460.26232790293699
1.997-2.02230.26161600.25052786294698
2.0223-2.04890.27021440.25272758290298
2.0489-2.0770.39561390.35132575271491
2.077-2.10660.27781450.23232766291198
2.1066-2.13810.22971490.20742767291699
2.1381-2.17150.22051360.19642825296199
2.1715-2.20710.2161620.18972771293399
2.2071-2.24520.2095870.18951719180690
2.2452-2.2860.23311250.19252286241182
2.286-2.32990.21331320.18032798293099
2.3299-2.37750.17881390.18032791293099
2.3775-2.42920.19541350.17042819295499
2.4292-2.48570.19251560.17332821297799
2.4857-2.54790.24451370.17172815295299
2.5479-2.61670.24131470.17332832297999
2.6167-2.69370.21741400.18932783292397
2.6937-2.78070.23781470.1692807295499
2.7807-2.880.21821340.17932848298299
2.88-2.99530.22381450.18132814295999
2.9953-3.13160.22351520.17432793294598
3.1316-3.29670.16871400.17372830297098
3.2967-3.50320.23471400.17752800294097
3.5032-3.77350.21231450.16872809295497
3.7735-4.15310.18971400.16282792293296
4.1531-4.75350.18891440.15262818296297
4.7535-5.98680.2081510.17172880303197
5.9868-45.99390.21671510.20542947309896
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)
10.4046-0.1545-0.12130.88450.05830.9287-0.00940.0146-0.0088-0.09740.02950.0173-0.00490.0745-00.2145-0.0035-0.00580.2360.00450.20289.073258.77682.4545
20.3606-0.01770.00490.8740.33040.71840.0165-0.0659-0.00870.13140.0164-0.02440.0459-0.00430.00010.1777-0.0106-0.0020.19620.00820.200488.9698219.5929-2.4712
30.5799-0.0398-0.00050.9505-0.3940.92540.00420.04370.0748-0.01430.10520.0452-0.0819-0.205100.2326-0.00670.01940.27580.02580.229684.982221.595731.9716
40.5248-0.05660.05110.6762-0.42331.1149-0.01580.06420.04750.00760.0575-0.0181-0.131-0.063300.24120.00120.01140.19550.01240.2007129.3556226.887331.8353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 24 through 265)A24 - 265
2X-RAY DIFFRACTION2(chain 'B' and resid 24 through 265)B24 - 265
3X-RAY DIFFRACTION3(chain 'C' and resid 24 through 265)C24 - 265
4X-RAY DIFFRACTION4(chain 'D' and resid 24 through 265)D24 - 265

+
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