[English] 日本語
Yorodumi
- PDB-1or0: Crystal Structures of Glutaryl 7-Aminocephalosporanic Acid Acylas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1or0
TitleCrystal Structures of Glutaryl 7-Aminocephalosporanic Acid Acylase: Insight into Autoproteolytic Activation
Components
  • Glutaryl 7-Aminocephalosporanic Acid Acylase
  • glutaryl acylase
KeywordsHYDROLASE / Glutaryl 7-aminocephalosporanic acid / N-terminal nucleophile (Ntn) hydrolases / Glutaryl 7-aminocephalosporanic acid Acylase
Function / homology
Function and homology information


glutaryl-7-aminocephalosporanic-acid acylase / glutaryl-7-aminocephalosporanic-acid acylase activity / antibiotic biosynthetic process / periplasmic space / response to antibiotic
Similarity search - Function
Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 / Penicillin amidase type, N-terminal domain, B-knob ...Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL acylase / 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 / Glutaryl-7-aminocephalosporanic-acid acylase
Similarity search - Component
Biological speciesPseudomonas sp. SY-77-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKim, J.K. / Yang, I.S. / Rhee, S. / Dauter, Z. / Lee, Y.S. / Park, S.S. / Kim, K.H.
CitationJournal: Biochemistry / Year: 2003
Title: Crystal Structures of Glutaryl 7-Aminocephalosporanic Acid Acylase: Insight into Autoproteolytic Activation
Authors: Kim, J.K. / Yang, I.S. / Rhee, S. / Dauter, Z. / Lee, Y.S. / Park, S.S. / Kim, K.H.
History
DepositionMar 11, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutaryl 7-Aminocephalosporanic Acid Acylase
B: glutaryl acylase
C: Glutaryl 7-Aminocephalosporanic Acid Acylase
D: glutaryl acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,6626
Polymers154,5384
Non-polymers1242
Water25,7431429
1
A: Glutaryl 7-Aminocephalosporanic Acid Acylase
B: glutaryl acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3313
Polymers77,2692
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8120 Å2
ΔGint-49 kcal/mol
Surface area24670 Å2
MethodPISA
2
C: Glutaryl 7-Aminocephalosporanic Acid Acylase
D: glutaryl acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3313
Polymers77,2692
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-50 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.667, 69.907, 113.726
Angle α, β, γ (deg.)90.00, 97.63, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Glutaryl 7-Aminocephalosporanic Acid Acylase


Mass: 17644.172 Da / Num. of mol.: 2 / Fragment: alpha subunit, RESIDUES 1-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. SY-77-1 (bacteria) / Strain: GK16 / Plasmid: pET23a / Production host: Escherichia coli (E. coli)
References: UniProt: Q84I62, UniProt: P07662*PLUS, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein glutaryl acylase / Glutaryl 7-Aminocephalosporanic Acid Acylase


Mass: 59624.598 Da / Num. of mol.: 2 / Fragment: beta subunit, RESIDUES 1-522
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. SY-77-1 (bacteria) / Strain: GK16 / Plasmid: pET23a / Production host: Escherichia coli (E. coli)
References: UniProt: Q84I62, UniProt: P07662*PLUS, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1429 / 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: 2.93 Å3/Da / Density % sol: 57.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.6M ammonium sulfate, 0.1M HEPES, and 0.1M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.6 Mammonium sulfate1reservoir
20.1 MHEPES1reservoirpH7.5
30.1 M1reservoirNaCl

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9810, 0.9800, 0.9680
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9811
20.981
30.9681
ReflectionResolution: 2→19.95 Å / Num. obs: 217224 / % possible obs: 91.8 %
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. obs: 110770

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→19.95 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.184 8392 0.2113 %RANDOM
Rwork0.171 ---
obs0.189 217224 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.824 Å2 / ksol: 0.389707 e/Å3
Displacement parametersBiso mean: 14.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.65 Å20 Å2-1.9 Å2
2--3.38 Å20 Å2
3----0.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10609 0 8 1429 12046
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.921.5
X-RAY DIFFRACTIONc_mcangle_it1.312
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.532.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.21 1291 3.9 %
Rwork0.212 32046 -
obs--84.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3EG.PARAMEG.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. reflection obs: 110770 / Num. reflection Rfree: 4488 / % reflection Rfree: 4 % / Rfactor Rfree: 0.206 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

+
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