[English] 日本語
Yorodumi
- PDB-5acq: W228A-Investigation of the impact from residues W228 and Y233 in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5acq
TitleW228A-Investigation of the impact from residues W228 and Y233 in the metallo-beta-lactamase GIM-1
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / METALLO-BETA-LACTAMASE / GIM-1 / CARBAPENEMASE / ENZYME KINETICS / MIC
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / periplasmic space / response to antibiotic / metal ion binding
Similarity search - Function
: / : / 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
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSkagseth, S. / Carlsen, T.J. / Bjerga, G.E.K. / Spencer, J. / Samuelsen, O. / Leiros, H.-K.S.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2015
Title: Role of Residues W228 and Y233 in the Structure and Activity of Metallo-Beta-Lactamase Gim-1.
Authors: Skagseth, S. / Carlsen, T.J. / Bjerga, G.E.K. / Spencer, J. / Samuelsen, O. / Leiros, H.S.
History
DepositionAug 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 2.0Oct 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-LACTAMASE
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9705
Polymers54,7742
Non-polymers1963
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-127.5 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.549, 131.796, 40.581
Angle α, β, γ (deg.)90.00, 95.51, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein BETA-LACTAMASE


Mass: 27387.045 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR PRARE / References: UniProt: Q704V1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.34 % / Description: NONE
Crystal growDetails: 19.8% POLYETHYLENE GLYCOL (PEG) 10K AND 0.1 M SODIUM CACODYLATE, PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.24
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.7→44 Å / Num. obs: 42445 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.2 / % possible all: 92.5

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YNT

2ynt


Resolution: 1.7→24.998 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 2137 5.1 %
Rwork0.1878 --
obs0.1897 42278 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→24.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 0 3 281 3649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123476
X-RAY DIFFRACTIONf_angle_d1.3784730
X-RAY DIFFRACTIONf_dihedral_angle_d13.8641260
X-RAY DIFFRACTIONf_chiral_restr0.053533
X-RAY DIFFRACTIONf_plane_restr0.007599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73950.29141360.2612575X-RAY DIFFRACTION92
1.7395-1.7830.33391550.2612593X-RAY DIFFRACTION94
1.783-1.83120.2291450.24392685X-RAY DIFFRACTION95
1.8312-1.88510.30251520.23272609X-RAY DIFFRACTION95
1.8851-1.94590.25511480.21242654X-RAY DIFFRACTION95
1.9459-2.01540.26491240.20882639X-RAY DIFFRACTION94
2.0154-2.09610.2321380.20132643X-RAY DIFFRACTION96
2.0961-2.19140.22511440.20062671X-RAY DIFFRACTION96
2.1914-2.30690.21831310.1942691X-RAY DIFFRACTION96
2.3069-2.45130.22531560.19862718X-RAY DIFFRACTION97
2.4513-2.64040.261480.20232679X-RAY DIFFRACTION96
2.6404-2.90570.27441450.20662727X-RAY DIFFRACTION97
2.9057-3.32540.24531230.19542760X-RAY DIFFRACTION98
3.3254-4.18640.21961610.16332726X-RAY DIFFRACTION98
4.1864-25.00020.1741310.16362771X-RAY DIFFRACTION97
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)
14.02480.82320.14067.34652.92516.27540.0759-0.0253-0.3826-0.22720.1455-0.33150.22820.1151-0.19890.14510.00480.02060.25880.01630.217421.8958-3.714116.5236
22.46740.01372.21061.82550.66873.27910.3026-0.5937-0.1951-0.0135-0.149-0.08580.1273-0.0788-0.14630.18510.02040.03090.38570.01670.202920.5325-3.951324.5675
35.4481-0.16241.87374.6421-1.90724.95850.3139-0.7352-0.22190.1921-0.19590.19840.0028-0.0291-0.09590.1956-0.0250.03440.4662-0.0090.14257.7575-2.427929.9423
44.6061.70521.18953.55571.50993.6567-0.00010.28960.2855-0.401-0.10150.2052-0.2409-0.31940.10850.23410.08210.00710.28010.0240.17198.24914.294910.6324
53.72643.48810.06436.43842.68812.7307-0.217-0.05270.8402-1.26780.41871.815-0.1307-0.71760.12520.5688-0.1317-0.37290.42150.150.84792.897-28.86034.7343
67.3242-1.1796-2.18793.2223-1.84222.87060.1312-0.45880.6109-0.2180.27710.60530.0447-0.3188-0.34740.3476-0.0685-0.02980.29240.08820.50725.0799-37.177611.2243
73.1022-0.1838-0.41614.3786-1.01913.2687-0.23860.2790.4226-1.21660.3031-0.41620.24810.1399-0.03380.6819-0.1569-0.01710.28340.0480.444717.6534-35.50421.3135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 39 THROUGH 88 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 89 THROUGH 124 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 125 THROUGH 175 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 179 THROUGH 295 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 40 THROUGH 76 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 77 THROUGH 124 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 125 THROUGH 295 )

+
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