[English] 日本語
Yorodumi
- PDB-3jtq: Mutations in Cephalosporin Acylase Affecting Stability and Autopr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3jtq
TitleMutations in Cephalosporin Acylase Affecting Stability and Autoproteolysis
Components(Glutaryl 7-aminocephalosporanic acid acylase) x 2
KeywordsHYDROLASE / cephalosporin acylase / Autoproteolysis
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / antibiotic biosynthetic process / periplasmic space
Similarity search - Function
Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 / Penicillin amidase type, N-terminal domain, B-knob ...Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 / Penicillin amidase type, N-terminal domain, B-knob / Penicillin amidase type, A-knob / Penicillin amidase / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutaryl 7-aminocephalosporanic acid acylase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCho, K.J. / Kim, J.K. / Lee, J.H. / Shin, H.J. / Park, S.S. / Kim, K.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Structural features of cephalosporin acylase reveal the basis of autocatalytic activation.
Authors: Cho, K.J. / Kim, J.K. / Lee, J.H. / Shin, H.J. / Park, S.S. / Kim, K.H.
History
DepositionSep 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutaryl 7-aminocephalosporanic acid acylase
B: Glutaryl 7-aminocephalosporanic acid acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8604
Polymers77,6762
Non-polymers1842
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint-53 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.836, 73.836, 384.184
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Glutaryl 7-aminocephalosporanic acid acylase


Mass: 18506.191 Da / Num. of mol.: 1 / Fragment: UNP residues 30-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: GK16 / Plasmid: pET23d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A4ZVL3, glutaryl-7-aminocephalosporanic-acid acylase
#2: Protein Glutaryl 7-aminocephalosporanic acid acylase


Mass: 59169.777 Da / Num. of mol.: 1 / Fragment: UNP residues 199-720 / Mutation: L210N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: GK16 / Plasmid: pET23d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A4ZVL3, glutaryl-7-aminocephalosporanic-acid acylase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DEPOSITORS STATE THAT UNIPROT IS INCORRECT AT THESE POSITIONS

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Na-cacodylate (pH 6.5), 0.2M magnesium chloride, PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 55819 / Num. obs: 53754 / % possible obs: 96.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 32.9
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 5 / % possible all: 90.4

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ADV

2adv


Resolution: 2.2→48.39 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.959 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2733 5.1 %RANDOM
Rwork0.209 ---
obs0.211 53658 96.31 %-
all-55714 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.19 Å2 / Biso mean: 34.323 Å2 / Biso min: 15.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5326 0 12 350 5688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225492
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.9417499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1985674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75523.238281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77115790
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5671550
X-RAY DIFFRACTIONr_chiral_restr0.0890.2782
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024416
X-RAY DIFFRACTIONr_nbd_refined0.2030.22655
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23777
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2399
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0730.212
X-RAY DIFFRACTIONr_mcbond_it0.7741.53444
X-RAY DIFFRACTIONr_mcangle_it1.27125431
X-RAY DIFFRACTIONr_scbond_it2.7832357
X-RAY DIFFRACTIONr_scangle_it2.9474.52068
X-RAY DIFFRACTIONr_rigid_bond_restr3.00435801
X-RAY DIFFRACTIONr_sphericity_free6.2663350
X-RAY DIFFRACTIONr_sphericity_bonded3.15835340
LS refinement shellResolution: 2.198→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 179 -
Rwork0.263 3452 -
all-3631 -
obs--90.03 %

+
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