[English] 日本語
Yorodumi
- PDB-1bls: CRYSTALLOGRAPHIC STRUCTURE OF A PHOSPHONATE DERIVATIVE OF THE ENT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bls
TitleCRYSTALLOGRAPHIC STRUCTURE OF A PHOSPHONATE DERIVATIVE OF THE ENTEROBACTER CLOACAE P99 CEPHALOSPORINASE: MECHANISTIC INTERPRETATION OF A BETA-LACTAMASE TRANSITION STATE ANALOG
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE (ACTING IN CYCLIC AMIDES)
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(P-IODOPHENYLACETYLAMINO)METHYLPHOSPHINIC ACID / Beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsKnox, J.R. / Moews, P.C. / Lobkovsky, E.
Citation
Journal: Biochemistry / Year: 1994
Title: Crystallographic structure of a phosphonate derivative of the Enterobacter cloacae P99 cephalosporinase: mechanistic interpretation of a beta-lactamase transition-state analog.
Authors: Lobkovsky, E. / Billings, E.M. / Moews, P.C. / Rahil, J. / Pratt, R.F. / Knox, J.R.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Evolution of an Enzyme Activity: Crystallographic Structure at 2 Angstroms Resolution of the Cephalosporinase from the Ampc Gene of Enterobacter Cloacae P99 and Comparison with a Class a Penicillinase
Authors: Lobkovsky, E. / Moews, P.C. / Liu, H. / Zhao, H. / Frere, J.M. / Knox, J.R.
History
DepositionDec 17, 1993Processing site: BNL
Revision 1.0May 8, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2184
Polymers78,5402
Non-polymers6782
Water14,214789
1
A: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6092
Polymers39,2701
Non-polymers3391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6092
Polymers39,2701
Non-polymers3391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.500, 83.470, 95.460
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999993, -0.000825, -0.003734), (0.000865, -0.999943, -0.010627), (-0.003725, -0.01063, 0.999937)
Vector: 23.3541, 56.1404, 0.9756)
DetailsTHE *MTRIX* RECORDS BELOW MAY BE USED TO GENERATE APPROXIMATE COORDINATES OF MOLECULE B WHEN APPLIED TO MOLECULE A.

-
Components

#1: Protein BETA-LACTAMASE


Mass: 39269.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / References: UniProt: P05364, beta-lactamase
#2: Chemical ChemComp-IPP / (P-IODOPHENYLACETYLAMINO)METHYLPHOSPHINIC ACID


Mass: 339.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11INO3P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 789 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTURN INFORMATION IS EASILY OBTAINED USING THE DSSP ANALYSIS PROGRAM BY KABSCH AND SANDER, ...TURN INFORMATION IS EASILY OBTAINED USING THE DSSP ANALYSIS PROGRAM BY KABSCH AND SANDER, BIOPOLYMERS 22, 2577 (1983).
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal grow
*PLUS
pH: 6.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
250 mMsodium cacodylate11
1PEG800011

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 28780 / % possible obs: 91 % / Num. measured all: 82494 / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
Highest resolution: 2.32 Å / Lowest resolution: 2.47 Å / % possible obs: 76 % / Num. unique obs: 7904 / Rmerge(I) obs: 0.158

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.3→8 Å /
RfactorNum. reflection
obs0.192 27532
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5502 0 50 789 6341
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d1.1
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.3 Å / Rfactor Rwork: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_planar_d0.040.017
X-RAY DIFFRACTIONp_chiral_restr0.150.113
X-RAY DIFFRACTIONp_scbond_it31.3
X-RAY DIFFRACTIONp_scangle_it4.52

+
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