[English] 日本語
Yorodumi
- PDB-2ynt: GIM-1-3Mol native. Crystal structures of Pseudomonas aeruginosa G... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ynt
TitleGIM-1-3Mol native. Crystal structures of Pseudomonas aeruginosa GIM- 1: active site plasticity in metallo-beta-lactamases
Components(GIM-1 PROTEIN) x 2
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE / RESIDUE DETERMINANTS / LOOP DYNAMICS
Function / homology
Function and homology information


antibiotic catabolic process / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / 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: 1.598 Å
AuthorsBorra, P.S. / Samuelsen, O. / Spencer, J. / Lorentzen, M.S. / Leiros, H.-K.S.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2013
Title: Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active-Site Plasticity in Metallo-Beta-Lactamases.
Authors: Borra, P.S. / Samuelsen, O. / Spencer, J. / Walsh, T.R. / Lorentzen, M.S. / Leiros, H.-K.S.
History
DepositionOct 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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: GIM-1 PROTEIN
B: GIM-1 PROTEIN
C: GIM-1 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,45011
Polymers76,8733
Non-polymers5778
Water13,872770
1
B: GIM-1 PROTEIN
hetero molecules

B: GIM-1 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5296
Polymers51,2682
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area1870 Å2
ΔGint-166 kcal/mol
Surface area18970 Å2
MethodPISA
2
A: GIM-1 PROTEIN
C: GIM-1 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6858
Polymers51,2402
Non-polymers4466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-165.3 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.922, 140.658, 41.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein GIM-1 PROTEIN / METALLO-BETA-LACTAMASE GIM-1


Mass: 25619.758 Da / Num. of mol.: 2 / Fragment: RESIDUES 19-250
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 PLYSS PRARE / References: UniProt: Q704V1
#2: Protein GIM-1 PROTEIN / METALLO-BETA-LACTAMASE GIM-1


Mass: 25633.785 Da / Num. of mol.: 1 / Fragment: RESIDUES 19-250
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 PLYSS PRARE / References: UniProt: Q704V1
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1-18 IN THE GENE SEQUENCE ARE REMOVED AND A HIS TAG AND TEV CLEAVE SITE WAS INTRODUCED. A ...RESIDUES 1-18 IN THE GENE SEQUENCE ARE REMOVED AND A HIS TAG AND TEV CLEAVE SITE WAS INTRODUCED. A SERINE FROM THE TEV SITE IS THEN THE FIRST RESIDUE FOLLOWED BY GLN19 IN THE GENE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.97 % / Description: NONE
Crystal growDetails: 0.1M TRIS PH 7.1, 21% POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000 (PEG MME 2K), 4% GLYCEROL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.24
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 84988 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 14.48 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 0
Reflection shellResolution: 1.6→1.68 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 0 / % possible all: 90.7

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DDK

1ddk


Resolution: 1.598→19.987 Å / SU ML: 0.14 / σ(F): 0.24 / Phase error: 18.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 4267 5 %
Rwork0.1622 --
obs0.1644 84751 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.598→19.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5153 0 18 770 5941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065509
X-RAY DIFFRACTIONf_angle_d1.1027519
X-RAY DIFFRACTIONf_dihedral_angle_d13.0052005
X-RAY DIFFRACTIONf_chiral_restr0.076835
X-RAY DIFFRACTIONf_plane_restr0.005967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.598-1.61620.27141280.21662196X-RAY DIFFRACTION83
1.6162-1.63520.23971160.19782371X-RAY DIFFRACTION88
1.6352-1.65510.23631320.19362461X-RAY DIFFRACTION91
1.6551-1.67610.2371320.1852566X-RAY DIFFRACTION96
1.6761-1.69810.24491310.17752662X-RAY DIFFRACTION98
1.6981-1.72130.23311560.18032681X-RAY DIFFRACTION100
1.7213-1.74590.24581310.17332682X-RAY DIFFRACTION100
1.7459-1.7720.21971450.16572690X-RAY DIFFRACTION99
1.772-1.79960.20971530.16442689X-RAY DIFFRACTION100
1.7996-1.82910.21131490.15922653X-RAY DIFFRACTION100
1.8291-1.86060.18311300.16022742X-RAY DIFFRACTION100
1.8606-1.89450.21081580.15972658X-RAY DIFFRACTION100
1.8945-1.93090.19711680.15752682X-RAY DIFFRACTION100
1.9309-1.97020.20681400.16022716X-RAY DIFFRACTION100
1.9702-2.0130.21241140.16232707X-RAY DIFFRACTION100
2.013-2.05980.18651380.16392746X-RAY DIFFRACTION100
2.0598-2.11130.21371510.16292651X-RAY DIFFRACTION100
2.1113-2.16830.21061410.16492743X-RAY DIFFRACTION100
2.1683-2.2320.2371160.16522730X-RAY DIFFRACTION100
2.232-2.3040.1981550.16472710X-RAY DIFFRACTION100
2.304-2.38620.24771380.16772721X-RAY DIFFRACTION100
2.3862-2.48160.20631530.16922709X-RAY DIFFRACTION100
2.4816-2.59430.21271400.17392753X-RAY DIFFRACTION99
2.5943-2.73070.22051300.16332743X-RAY DIFFRACTION100
2.7307-2.90130.17971500.16512733X-RAY DIFFRACTION100
2.9013-3.12460.22111420.17322766X-RAY DIFFRACTION100
3.1246-3.43760.22991600.15752760X-RAY DIFFRACTION100
3.4376-3.93170.17861450.14412778X-RAY DIFFRACTION100
3.9317-4.94120.16171600.1352823X-RAY DIFFRACTION100
4.9412-19.98810.19281650.16512962X-RAY DIFFRACTION100

+
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