[English] 日本語
Yorodumi
- PDB-7kd9: Crystal Structure of Gallic Acid Decarboxylase from Arxula adenin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kd9
TitleCrystal Structure of Gallic Acid Decarboxylase from Arxula adeninivorans
ComponentsGallate decarboxylase
KeywordsLYASE / Decarboxylase
Function / homologySnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / : / ARAD1C45716p
Function and homology information
Biological speciesBlastobotrys adeninivorans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsZeug, M. / Markovic, N. / Iancu, C.V. / Tripp, J. / Oreb, M. / Choe, J.
CitationJournal: Sci Rep / Year: 2021
Title: Crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists.
Authors: Zeug, M. / Markovic, N. / Iancu, C.V. / Tripp, J. / Oreb, M. / Choe, J.Y.
History
DepositionOct 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gallate decarboxylase
B: Gallate decarboxylase
C: Gallate decarboxylase
D: Gallate decarboxylase
E: Gallate decarboxylase
F: Gallate decarboxylase
G: Gallate decarboxylase
H: Gallate decarboxylase
I: Gallate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,29512
Polymers245,1789
Non-polymers1173
Water13,709761
1
A: Gallate decarboxylase
B: Gallate decarboxylase
D: Gallate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7654
Polymers81,7263
Non-polymers391
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10310 Å2
ΔGint-50 kcal/mol
Surface area23890 Å2
MethodPISA
2
C: Gallate decarboxylase
E: Gallate decarboxylase
F: Gallate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7654
Polymers81,7263
Non-polymers391
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10100 Å2
ΔGint-48 kcal/mol
Surface area24370 Å2
MethodPISA
3
G: Gallate decarboxylase
H: Gallate decarboxylase
I: Gallate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7654
Polymers81,7263
Non-polymers391
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10030 Å2
ΔGint-47 kcal/mol
Surface area24890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.632, 265.301, 93.728
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

#1: Protein
Gallate decarboxylase / ARAD1C45716p


Mass: 27241.947 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blastobotrys adeninivorans (fungus) / Gene: AGDC1, GNLVRS02_ARAD1C45716g / Production host: Escherichia coli (E. coli) / References: UniProt: A0A060TAG5
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 761 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 3350, KSCN, MES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-BM-B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 168891 / % possible obs: 99.51 % / Redundancy: 4.9 % / Biso Wilson estimate: 33.46 Å2 / Rsym value: 0.09 / Net I/σ(I): 15.2
Reflection shellResolution: 1.94→2 Å / Redundancy: 4.2 % / Num. unique obs: 16310 / Rsym value: 0.902 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7jmr

7jmr


Resolution: 1.94→46.61 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2375 8291 4.91 %
Rwork0.191 160518 -
obs0.1933 168809 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.44 Å2 / Biso mean: 50.2847 Å2 / Biso min: 16.93 Å2
Refinement stepCycle: final / Resolution: 1.94→46.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16819 0 3 761 17583
Biso mean--27.05 43.81 -
Num. residues----2027
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.94-1.960.33452400.29264921516192
1.96-1.980.3432890.28115247553699
1.98-2.010.30722240.26853265550100
2.01-2.030.31942700.2653175587100
2.03-2.060.29612630.243952775540100
2.06-2.090.30562530.233553525605100
2.09-2.120.26132890.233552765565100
2.12-2.150.26722360.235854085644100
2.15-2.180.27922380.239653755613100
2.18-2.220.29262810.224152995580100
2.22-2.260.25373330.218152405573100
2.26-2.30.23672820.212453095591100
2.3-2.340.263300.21655261559199
2.34-2.390.29062590.209552945553100
2.39-2.440.24472410.208753665607100
2.44-2.50.26242610.20253365597100
2.5-2.560.28452910.20553605651100
2.56-2.630.29382760.209553365612100
2.63-2.710.25413120.204353375649100
2.71-2.80.25162460.199953805626100
2.8-2.90.27892920.209853695661100
2.9-3.010.27122840.206553555639100
3.01-3.150.2392690.19854125681100
3.15-3.320.22852720.190953925664100
3.32-3.520.22892950.189953975692100
3.52-3.790.2263150.174653915706100
3.8-4.180.2143040.157654075711100
4.18-4.780.16982750.14754905765100
4.78-6.020.22722780.158655325810100
6.02-46.610.19652930.181757566049100
Refinement TLS params.Method: refined / Origin x: 98.0768 Å / Origin y: 38.0882 Å / Origin z: 56.9198 Å
111213212223313233
T0.1977 Å20.0061 Å2-0.0381 Å2-0.212 Å20.0648 Å2--0.1841 Å2
L0.2611 °20.1466 °2-0.1138 °2-0.3347 °20.1014 °2--0.1287 °2
S-0.0215 Å °-0.0092 Å °-0.0475 Å °0.0173 Å °-0.0354 Å °-0.0381 Å °0.024 Å °0.0035 Å °-0.0189 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 231
2X-RAY DIFFRACTION1allB6 - 230
3X-RAY DIFFRACTION1allC5 - 231
4X-RAY DIFFRACTION1allD6 - 231
5X-RAY DIFFRACTION1allE11 - 229
6X-RAY DIFFRACTION1allF6 - 230
7X-RAY DIFFRACTION1allG6 - 231
8X-RAY DIFFRACTION1allH9 - 230
9X-RAY DIFFRACTION1allI5 - 230
10X-RAY DIFFRACTION1allJ1 - 3
11X-RAY DIFFRACTION1allS1 - 761

+
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://pdbjlvh1.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