[English] 日本語
Yorodumi
- PDB-7q0y: Crystal structure of CTX-M-14 in complex with Bortezomib -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q0y
TitleCrystal structure of CTX-M-14 in complex with Bortezomib
ComponentsBeta-lactamase
KeywordsHYDROLASE / Lactamase / Antibiotic / Resistence
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-BO2 / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsWerner, N. / Perbandt, M. / Hinrichs, W. / Prester, A. / Rohde, H. / Aepfelbacher, M. / Betzel, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
CitationJournal: Sci Rep / Year: 2022
Title: Structural basis to repurpose boron-based proteasome inhibitors Bortezomib and Ixazomib as beta-lactamase inhibitors.
Authors: Perbandt, M. / Werner, N. / Prester, A. / Rohde, H. / Aepfelbacher, M. / Hinrichs, W. / Betzel, C.
History
DepositionOct 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 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: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5725
Polymers28,0021
Non-polymers5714
Water8,377465
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-15 kcal/mol
Surface area10710 Å2
Unit cell
Length a, b, c (Å)41.303, 62.331, 86.244
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

-
Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase


Mass: 28001.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2S1JJX2, beta-lactamase

-
Non-polymers , 5 types, 469 molecules

#2: Chemical ChemComp-BO2 / N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE / BORTEZOMIB


Mass: 384.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25BN4O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 1.98 Å3/Da / Density % sol: 37.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 30 % PEG8000, 0.2 M lithium sulfate, 0.1 M sodium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.3→35.46 Å / Num. obs: 55064 / % possible obs: 99 % / Redundancy: 7.1 % / Biso Wilson estimate: 9.85 Å2 / CC1/2: 1 / Rrim(I) all: 0.073 / Net I/σ(I): 16.89
Reflection shellResolution: 1.3→1.35 Å / Mean I/σ(I) obs: 3.59 / Num. unique obs: 38038 / CC1/2: 0.971 / Rrim(I) all: 0.527 / % possible all: 93

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GTH

6gth


Resolution: 1.3→43.12 Å / SU ML: 0.0889 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.8874
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1439 3791 3.62 %
Rwork0.1278 100865 -
obs0.1284 104656 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.2 Å2
Refinement stepCycle: LAST / Resolution: 1.3→43.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1961 0 39 465 2465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01022068
X-RAY DIFFRACTIONf_angle_d1.22382823
X-RAY DIFFRACTIONf_chiral_restr0.086334
X-RAY DIFFRACTIONf_plane_restr0.0133372
X-RAY DIFFRACTIONf_dihedral_angle_d13.8236768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.23291310.22213404X-RAY DIFFRACTION90.11
1.31-1.330.20171340.20183630X-RAY DIFFRACTION95.03
1.33-1.350.18511360.19453633X-RAY DIFFRACTION96.96
1.35-1.370.23191380.19923644X-RAY DIFFRACTION95.99
1.37-1.390.18741350.18263733X-RAY DIFFRACTION97.48
1.39-1.410.18211420.18283700X-RAY DIFFRACTION98.24
1.41-1.430.1851390.16763713X-RAY DIFFRACTION97.79
1.43-1.460.1751410.16113775X-RAY DIFFRACTION99.37
1.46-1.490.1851410.1523717X-RAY DIFFRACTION98.32
1.49-1.510.16871430.14843802X-RAY DIFFRACTION99.5
1.51-1.550.17971400.14463738X-RAY DIFFRACTION98.88
1.55-1.580.18091350.14033758X-RAY DIFFRACTION99.34
1.58-1.620.14921410.13463758X-RAY DIFFRACTION99.19
1.62-1.660.16981440.13473792X-RAY DIFFRACTION99.14
1.66-1.70.15431420.13193761X-RAY DIFFRACTION99.74
1.7-1.750.13171380.12343789X-RAY DIFFRACTION99.47
1.75-1.810.14821450.12223782X-RAY DIFFRACTION99.62
1.81-1.870.13841410.12413836X-RAY DIFFRACTION99.62
1.87-1.950.14731400.11533697X-RAY DIFFRACTION99.43
1.95-2.040.11471460.11123793X-RAY DIFFRACTION99.34
2.04-2.140.13051410.10633771X-RAY DIFFRACTION99.57
2.14-2.280.13071420.10453803X-RAY DIFFRACTION99.57
2.28-2.450.11091460.10993758X-RAY DIFFRACTION99.72
2.45-2.70.11311410.1153778X-RAY DIFFRACTION99.54
2.7-3.090.11561410.11233763X-RAY DIFFRACTION98.94
3.09-3.890.13161470.11023762X-RAY DIFFRACTION99.62
3.89-43.120.15161410.12883775X-RAY DIFFRACTION99.21
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)
12.242631997541.0678269041-0.1123920247662.384693648920.9471627297672.44277666126-0.05887054368320.184078313518-0.0971515031343-0.1269235733260.103408838669-0.05126017684040.05809480269860.0806345683458-0.04060379387180.06587954325790.00585748388033-0.005935159942070.0516384481753-0.005109529743330.050023978370310.3171912437-15.5004951166-22.9188347372
20.982560643037-0.41688674931-0.4060541385190.7365133163560.4798571487760.811863490091-0.0355574140764-0.00567605002975-0.1110348835320.0498281481725-0.01945570002720.06601252810950.0920477665441-0.0202499510550.05400630581980.0798092471365-0.004961743984610.003560777498270.07162273017850.005343919015530.06435193744482.61522473551-9.48363007832-7.57269694484
36.775036166394.04237973956-2.077384062764.48942275891-0.1568511242891.854051713970.243496075938-0.5712033460260.39848944410.292983894758-0.2998855074890.3584366729680.02038468620920.07484838158180.04083469104040.100982371535-0.005589703586880.0101308754740.111262240271-0.01921070271920.0662675430427-3.8884307101610.358261696.19459880402
42.561418998990.163857727503-0.9971422678791.027783819780.0962615554031.000162111310.087562966817-0.07576302066830.2654597523820.0391363041031-0.01194372260420.0225301777299-0.121088507920.0378322586745-0.06705345643240.077440401396-0.0007544841192880.0006709845643930.0703323132087-0.008582577711060.07326596958211.1434130236613.2695606968-3.2232998709
50.706980260374-0.218218718148-0.1479301625170.5423328626010.02173197537770.291438998712-0.0190017313104-0.125398802207-0.03498393403080.06122434821080.0231524890398-0.007163099525470.007414595207170.046581393722-0.006024834205090.091884345818-0.0015789568098-0.008402067267090.1052166345160.003061782983490.07176731316388.47697187935-2.06672819682-0.280932673953
68.33951764178-3.024756240191.198380148971.33347206392-0.05166751476181.1569965576-0.003048112851660.00353182948258-0.233612344623-0.0423982135537-0.00715277323680.1239961945280.0679331957802-0.04006253732320.02277874447370.0700757222151-0.007963868132860.004857347481490.05712307800210.01045852003590.04471413594071.07623305626-12.2917578623-7.74829888613
71.000254865980.103664034926-0.1201356716120.526444144298-0.001590960740760.3237781111840.002936365924870.12990562775-0.0195612914958-0.07540235732650.03645521218430.04145522664030.0477290040645-0.104149019201-0.02424799093660.068597379265-0.00609401151944-0.0129388903540.07984534171170.0004151113828240.0488970234149-6.55018719969-2.31259515025-13.3872717754
84.360376066380.1625314254720.4340398787030.803368303961-0.1574797027650.948235491174-0.02811469911680.0921133588739-0.0436020843212-0.04722265305050.02172169785490.00223622898408-0.00508306621178-0.008531587072290.01844212050590.06128123367930.00343609879597-0.003751930384950.0514433487583-0.01168929821840.02753600907276.16314008705-4.43055320684-16.9101016371
97.624503991425.927145027142.242793925867.456429951882.365690779975.99690832888-0.1496151367510.199425653024-0.0310436861629-0.2362976671970.02952046709470.1845419448360.102252593861-0.160953421380.08421650874260.07856879466740.00501105810773-0.002808589931970.0873279022826-0.01449146042340.06367414839054.0699808649-8.33679255305-25.636300796
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 25 through 50 )25 - 501 - 26
22chain 'A' and (resid 51 through 85 )51 - 8527 - 60
33chain 'A' and (resid 86 through 101 )86 - 10161 - 76
44chain 'A' and (resid 102 through 128 )102 - 12877 - 103
55chain 'A' and (resid 129 through 179 )129 - 179104 - 154
66chain 'A' and (resid 180 through 194 )180 - 194155 - 169
77chain 'A' and (resid 195 through 229 )195 - 229170 - 204
88chain 'A' and (resid 230 through 274 )230 - 274205 - 248
99chain 'A' and (resid 275 through 289 )275 - 289249 - 263

+
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