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- PDB-6w54: Crystal Structure of Gallic Acid Decarboxylase from Arxula adenin... -

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Basic information

Entry
Database: PDB / ID: 6w54
TitleCrystal Structure of Gallic Acid Decarboxylase from Arxula adeninivorans
ComponentsGallate decarboxylase
KeywordsLYASE / Decarboxylase
Function / homologySnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / 4-NITROCATECHOL / : / : / ARAD1C45716p
Function and homology information
Biological speciesBlastobotrys adeninivorans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsZeug, M. / Marckovic, 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
DepositionMar 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gallate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4954
Polymers27,2421
Non-polymers2533
Water3,351186
1
A: Gallate decarboxylase
hetero molecules

A: Gallate decarboxylase
hetero molecules

A: Gallate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,48512
Polymers81,7263
Non-polymers7599
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area11210 Å2
ΔGint-58 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.971, 81.971, 103.055
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-302-

K

21A-523-

HOH

31A-527-

HOH

41A-547-

HOH

51A-562-

HOH

61A-578-

HOH

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Components

#1: Protein Gallate decarboxylase / ARAD1C45716p


Mass: 27241.947 Da / Num. of mol.: 1
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-4NC / 4-NITROCATECHOL


Mass: 155.108 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 3350, Potassium Formate, MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 36574 / % possible obs: 88.5 % / Redundancy: 4.1 % / CC1/2: 0.95 / Rpim(I) all: 0.044 / Rrim(I) all: 0.094 / Rsym value: 0.094 / Net I/σ(I): 43
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2 % / Mean I/σ(I) obs: 5.8 / Num. unique obs: 689 / CC1/2: 0.819 / Rpim(I) all: 0.236 / Rrim(I) all: 0.357 / Rsym value: 0.308 / % possible all: 33.8

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Processing

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

Resolution: 1.5→41.7 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1662 -5 %
Rwork0.1402 --
obs0.1414 36568 88.4 %
Displacement parametersBiso mean: 24.93 Å2
Refinement stepCycle: LAST / Resolution: 1.5→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 13 186 2032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781913
X-RAY DIFFRACTIONf_angle_d0.98082590
X-RAY DIFFRACTIONf_chiral_restr0.0809260
X-RAY DIFFRACTIONf_plane_restr0.0074326
X-RAY DIFFRACTIONf_dihedral_angle_d17.3957697

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