[English] 日本語
Yorodumi
- PDB-7ljk: Crystal structure of the deacylation deficient KPC-2 F72Y mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ljk
TitleCrystal structure of the deacylation deficient KPC-2 F72Y mutant
ComponentsBeta-lactamase
KeywordsHYDROLASE / KPC / Carbapenemase / Beta-lactamase / Antibiotic Resistance / Enzyme / Beta-lactam / antibiotics
Function / homologyBeta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / beta-lactam antibiotic catabolic process / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like / beta-lactamase activity / beta-lactamase / response to antibiotic / beta-lactamase
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsFurey, I. / Palzkill, T. / Sankaran, B. / Hu, L. / Prasad, B.V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI32956 United States
Citation
Journal: J.Biol.Chem. / Year: 2021
Title: Local interactions with the Glu166 base and the conformation of an active site loop play key roles in carbapenem hydrolysis by the KPC-2 beta-lactamase.
Authors: Furey, I.M. / Mehta, S.C. / Sankaran, B. / Hu, L. / Prasad, B.V.V. / Palzkill, T.
#1: Journal: J Med Chem / Year: 2018
Title: Strategic Approaches to Overcome Resistance against Gram-Negative Pathogens Using Beta-Lactamase Inhibitors and Beta-Lactam Enhancers: Activity of Three Novel Diazabicyclooctanes WCK 5153, ...Title: Strategic Approaches to Overcome Resistance against Gram-Negative Pathogens Using Beta-Lactamase Inhibitors and Beta-Lactam Enhancers: Activity of Three Novel Diazabicyclooctanes WCK 5153, Zidebactam (WCK 5107), and WCK 4234.
Authors: Papp-Wallace, K.M. / Nguyen, N.Q. / Jacobs, M.R. / Bethel, C.R. / Barnes, M.D. / Kumar, V. / Bajaksouzian, S. / Rudin, S.D. / Rather, P.N. / Bhavsar, S. / Ravikumar, T. / Deshpande, P.K. / ...Authors: Papp-Wallace, K.M. / Nguyen, N.Q. / Jacobs, M.R. / Bethel, C.R. / Barnes, M.D. / Kumar, V. / Bajaksouzian, S. / Rudin, S.D. / Rather, P.N. / Bhavsar, S. / Ravikumar, T. / Deshpande, P.K. / Patil, V. / Yeole, R. / Bhagwat, S.S. / Patel, M.V. / van den Akker, F. / Bonomo, R.A.
History
DepositionJan 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 30, 2021Group: Structure summary / Category: audit_author
Revision 1.3Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.4Oct 18, 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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)56,0172
Polymers56,0172
Non-polymers00
Water7,098394
1
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)28,0091
Polymers28,0091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)28,0091
Polymers28,0091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.325, 37.310, 82.178
Angle α, β, γ (deg.)92.430, 90.413, 94.617
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein Beta-lactamase


Mass: 28008.506 Da / Num. of mol.: 2 / Mutation: F72Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: KPC-2, bla, bla_1, bla_4, blaKPC, blaKPC-2, kpc2, B4U25_43300, BANRA_05566, C2U49_28140, C3F39_16210, C3F39_28515, C3F39_28975, C4Y50_021815, CK508_026140, DM059_13800, DM060_30440, DM078_ ...Gene: KPC-2, bla, bla_1, bla_4, blaKPC, blaKPC-2, kpc2, B4U25_43300, BANRA_05566, C2U49_28140, C3F39_16210, C3F39_28515, C3F39_28975, C4Y50_021815, CK508_026140, DM059_13800, DM060_30440, DM078_27040, DN589_26110, EAO17_31575, FKC87_27985, GF489_24625, GS419_28405, IPF_358, KP64477d_00006, KPC_069, p628KPC_020, pCRE79_15, pCT-KPC_129, pFOS18_014, pkp469IL_0095, pkp53il_00095, SAMEA3649709_04840, SAMEA3649772_05181, UC330_005, UC332_005, UC334_005
Production host: Escherichia coli (E. coli) / References: UniProt: Q93LQ9, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 25% PEG 8,000, 0.1M KsCN, 0.1M Sodium Acetate pH:4.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.81→37.15 Å / Num. obs: 32888 / % possible obs: 88.88 % / Redundancy: 1.8 % / Biso Wilson estimate: 6.99 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.05725 / Net I/σ(I): 10.84
Reflection shellResolution: 1.81→1.875 Å / Num. unique obs: 3244 / CC1/2: 0.8763

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
xia2data reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C5A

3c5a


Resolution: 1.81→37.15 Å / SU ML: 0.1465 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.4234 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1971 1599 4.86 %
Rwork0.1567 31283 -
obs0.1586 32882 88.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.75 Å2
Refinement stepCycle: LAST / Resolution: 1.81→37.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3936 0 0 394 4330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714018
X-RAY DIFFRACTIONf_angle_d0.90315476
X-RAY DIFFRACTIONf_chiral_restr0.0572624
X-RAY DIFFRACTIONf_plane_restr0.0067714
X-RAY DIFFRACTIONf_dihedral_angle_d3.03062390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.870.20411550.14582789X-RAY DIFFRACTION87.85
1.87-1.940.21530.15352770X-RAY DIFFRACTION86.66
1.94-2.010.18881420.15522795X-RAY DIFFRACTION87.44
2.01-2.10.20981430.15872854X-RAY DIFFRACTION89.41
2.1-2.220.2151310.15452872X-RAY DIFFRACTION89.27
2.22-2.350.23071260.1542878X-RAY DIFFRACTION89.17
2.35-2.540.17961400.15442835X-RAY DIFFRACTION88.33
2.54-2.790.19471220.15782851X-RAY DIFFRACTION88.56
2.79-3.190.1931430.16182822X-RAY DIFFRACTION88.56
3.19-4.020.16781480.15613010X-RAY DIFFRACTION93.35
4.02-37.150.21031960.16162807X-RAY DIFFRACTION89.24
Refinement TLS params.Method: refined / Origin x: 16.5512149977 Å / Origin y: 13.6164919473 Å / Origin z: 8.93250055521 Å
111213212223313233
T0.00249997392642 Å20.010596463347 Å20.0219221783564 Å2-0.0311820394859 Å20.00785163919 Å2--0.0295471804217 Å2
L0.265229424011 °20.14213175909 °20.247089711054 °2-0.30949282892 °20.185717698157 °2--0.36697320723 °2
S0.000305422929084 Å °0.016488324391 Å °0.00279712896233 Å °0.0267030734765 Å °-0.00244435007744 Å °0.0080672968123 Å °-0.00915837642323 Å °0.0215165156885 Å °-0.00165960553335 Å °
Refinement TLS groupSelection details: all

+
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