[English] 日本語
Yorodumi
- PDB-3sw3: EDTA-free crystal structure of the mutant C221D of carbapenemase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sw3
TitleEDTA-free crystal structure of the mutant C221D of carbapenemase CphA from Aeromonas hydrophila
ComponentsBeta-lactamase
KeywordsHYDROLASE
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 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like ...Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsDelbruck, H. / Hoffmann, K.M.V.
CitationJournal: To be Published
Title: EDTA-free crystal structure of the mutant C221D of carbapenemase CphA from Aeromonas hydrophila
Authors: Delbruck, H. / Bebrone, C. / Hoffmann, K.M.V. / Galleni, M.
History
DepositionJul 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)25,2331
Polymers25,2331
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.622, 65.021, 67.272
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Beta-lactamase / carbapenemase CphA


Mass: 25232.764 Da / Num. of mol.: 1 / Fragment: UNP residues 28-254 / Mutation: C221D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: cphA / Plasmid: pET9a-CphA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P26918, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 277 K / pH: 4.6
Details: 0.05 M sodium acetate, 0.05 M potassium phosphate monobasic, 20% PEG8000, 2 mM zinc chloride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 9, 2009 / Details: MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→19.61 Å / Num. obs: 9845 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 33.33 Å2 / Rsym value: 0.069 / Net I/σ(I): 16.3
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 5.2 / Rsym value: 0.264 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0110refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X8G

1x8g


Resolution: 2.35→19.61 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.883 / SU B: 17.893 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.388 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 469 4.8 %RANDOM
Rwork0.189 ---
obs0.192 9323 99 %-
all-9802 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.695 Å2
Baniso -1Baniso -2Baniso -3
1-3.62 Å20 Å20 Å2
2---0.47 Å20 Å2
3----3.15 Å2
Refinement stepCycle: LAST / Resolution: 2.35→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 0 0 110 1723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221673
X-RAY DIFFRACTIONr_bond_other_d00.021127
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.9582280
X-RAY DIFFRACTIONr_angle_other_deg1.04332756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1415210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27323.91974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24215277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.951159
X-RAY DIFFRACTIONr_chiral_restr0.1020.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211861
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02337
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7461.51028
X-RAY DIFFRACTIONr_mcbond_other0.2091.5417
X-RAY DIFFRACTIONr_mcangle_it1.2721670
X-RAY DIFFRACTIONr_scbond_it2.1413645
X-RAY DIFFRACTIONr_scangle_it3.2174.5607
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 41 -
Rwork0.186 653 -
obs--97.88 %
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)
10.77580.9-0.8152.6571-1.43152.4616-0.0107-0.1831-0.05480.10380.0463-0.114-0.12020.2305-0.03560.1364-0.009-0.00270.2125-0.01080.183523.994.98818.303
21.28060.69920.33471.59421.85160.24450.0492-0.0380.00050.031-0.03410.0145-0.0582-0.0713-0.01520.17510.00820.00410.1813-0.00220.164615.3027.60118.711
36.53380.37434.32794.36384.01912.0536-0.0022-0.14690.2215-0.3155-0.18860.0601-0.07610.31860.19070.2668-0.03560.00060.1985-0.02730.114518.64917.4520.756
40.85990.8328-0.4678-0.07350.33441.801-0.0604-0.0285-0.0085-0.0670.10360.0591-0.118-0.0952-0.04320.19930.0315-0.0050.1861-0.00560.156311.4784.99811.96
51.8881.8053-0.47941.3586-2.84844.6363-0.03550.1471-0.1049-0.1959-0.11350.00310.1703-0.26050.1490.14260.017-0.00820.2149-0.02710.19477.009-2.8363.619
66.5706-3.64483.06858.5878-3.47453.6989-0.0819-0.4095-0.35420.02790.37560.1760.3065-0.3566-0.29380.1493-0.04680.00910.163-0.02090.12437.382-8.98817.478
72.2731-0.49551.28922.3905-0.10292.25510.3140.3058-0.0945-0.2118-0.1549-0.0519-0.4505-0.2382-0.15910.25840.0442-0.02440.14650.00260.122913.1618.8591.165
89.01592.5387.346619.5203-22.85113.2537-0.37290.51820.4261-0.624-0.1841-0.6995-0.15640.78890.55690.2765-0.03280.04770.1030.02960.187423.72413.6192.092
9-0.823-1.4013-0.38040.61591.20941.06620.0588-0.0322-0.0698-0.2031-0.1112-0.1022-0.03950.11760.05240.1595-0.0219-0.00520.2020.00860.188424.0341.5162.507
105.72-3.1869-3.76419.5697-2.15316.8914-0.1401-0.12580.05740.2855-0.191-0.75230.20270.36930.33110.0597-0.0123-0.01630.20910.02830.202532.25-3.5456.544
113.495-0.35211.82662.2157-1.10023.5591-0.03560.3059-0.1719-0.16010.0632-0.07960.50350.2866-0.02750.13730.04140.05570.1930.00810.170229.841-8.509-1.272
125.07860.6312-5.30823.1904-0.046614.20150.04860.0302-0.19660.0991-0.1517-0.4309-0.18130.67110.1031-0.0124-0.01810.00560.1817-0.01180.206931.7781.2334.195
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A41 - 76
2X-RAY DIFFRACTION2A77 - 98
3X-RAY DIFFRACTION3A99 - 109
4X-RAY DIFFRACTION4A110 - 136
5X-RAY DIFFRACTION5A137 - 152
6X-RAY DIFFRACTION6A153 - 170
7X-RAY DIFFRACTION7A171 - 183
8X-RAY DIFFRACTION8A184 - 189
9X-RAY DIFFRACTION9A190 - 216
10X-RAY DIFFRACTION10A217 - 231
11X-RAY DIFFRACTION11A232 - 249
12X-RAY DIFFRACTION12A250 - 264

+
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