[English] 日本語
Yorodumi
- PDB-3bgt: Structural Studies of Acetoacetate Decarboxylase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bgt
TitleStructural Studies of Acetoacetate Decarboxylase
ComponentsProbable acetoacetate decarboxylase
KeywordsLYASE / acetoacetate decarboxylase / Schiff base
Function / homology
Function and homology information


acetoacetate decarboxylase / acetoacetate decarboxylase activity
Similarity search - Function
Acetoacetate decarboxylase, bacterial / Acetoacetate decarboxylase-like / Acetoacetate decarboxylase-like / Acetoacetate decarboxylase / Acetoacetate decarboxylase domain superfamily / Acetoacetate decarboxylase (ADC) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Acetoacetate decarboxylase
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsHo, M. / Allen, K.N.
CitationJournal: Nature / Year: 2009
Title: The origin of the electrostatic perturbation in acetoacetate decarboxylase.
Authors: Ho, M.C. / Menetret, J.F. / Tsuruta, H. / Allen, K.N.
History
DepositionNov 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable acetoacetate decarboxylase
B: Probable acetoacetate decarboxylase
C: Probable acetoacetate decarboxylase
D: Probable acetoacetate decarboxylase


Theoretical massNumber of molelcules
Total (without water)110,6314
Polymers110,6314
Non-polymers00
Water7,350408
1
A: Probable acetoacetate decarboxylase
B: Probable acetoacetate decarboxylase
C: Probable acetoacetate decarboxylase
D: Probable acetoacetate decarboxylase

A: Probable acetoacetate decarboxylase
B: Probable acetoacetate decarboxylase
C: Probable acetoacetate decarboxylase
D: Probable acetoacetate decarboxylase

A: Probable acetoacetate decarboxylase
B: Probable acetoacetate decarboxylase
C: Probable acetoacetate decarboxylase
D: Probable acetoacetate decarboxylase


Theoretical massNumber of molelcules
Total (without water)331,89312
Polymers331,89312
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area49300 Å2
ΔGint-280 kcal/mol
Surface area92980 Å2
MethodPISA
2
A: Probable acetoacetate decarboxylase
B: Probable acetoacetate decarboxylase


Theoretical massNumber of molelcules
Total (without water)55,3152
Polymers55,3152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-30 kcal/mol
Surface area18520 Å2
MethodPISA
3
C: Probable acetoacetate decarboxylase

D: Probable acetoacetate decarboxylase


Theoretical massNumber of molelcules
Total (without water)55,3152
Polymers55,3152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area5110 Å2
ΔGint-28 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.447, 105.447, 252.379
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein
Probable acetoacetate decarboxylase / ADC / AAD


Mass: 27657.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Gene: adc / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q7NSA6, acetoacetate decarboxylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 291 K / Method: hanging drop / pH: 7.7
Details: 0.5M potassium phosphate dibasic/sodium phoshpate monobasic, pH 7.7, hanging drop, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: Quantum-315 / Detector: CCD / Date: Mar 28, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.99→30.3 Å / Num. obs: 133725

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.004data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
CNSrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.1→30.3 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.281 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 5659 9.8 %RANDOM
Rwork0.201 ---
obs0.201 114728 94.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.375 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7674 0 0 408 8082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0227873
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.98810721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.155973
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.09922.575334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.428151246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7911566
X-RAY DIFFRACTIONr_chiral_restr0.2360.21186
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026062
X-RAY DIFFRACTIONr_nbd_refined0.2710.23813
X-RAY DIFFRACTIONr_nbtor_refined0.3190.25295
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2556
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.2169
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.240
X-RAY DIFFRACTIONr_mcbond_it2.1841.54925
X-RAY DIFFRACTIONr_mcangle_it3.58927973
X-RAY DIFFRACTIONr_scbond_it3.76632948
X-RAY DIFFRACTIONr_scangle_it5.0794.52748
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 330 -
Rwork0.272 3439 -
all-3769 -
obs--83.7 %

+
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