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- PDB-7kd9: Crystal Structure of Gallic Acid Decarboxylase from Arxula adenin... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 49.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 3350, KSCN, MES

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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

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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

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