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- PDB-7pda: Crystal structure of Phenazine 1-carboxylic acid decarboxylase fr... -

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Basic information

Entry
Database: PDB / ID: 7pda
TitleCrystal structure of Phenazine 1-carboxylic acid decarboxylase from Mycobacterium fortuitum
Components
  • UNK
  • UbiD family decarboxylase
KeywordsLYASE / Phenazine 1-Carboxylic acid / UbiD / prFMN
Function / homologyUbiD decarboxylyase family / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain / carboxy-lyase activity / Chem-4LU / : / UbiD family decarboxylase
Function and homology information
Biological speciesMycolicibacterium fortuitum (bacteria)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsGahloth, D. / Leys, D.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: Crystal structure of Phenazine 1-carboxylic acid decarboxylase from Mycobacterium fortuitum
Authors: Gahloth, D. / Leys, D.
History
DepositionAug 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UbiD family decarboxylase
B: UNK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2385
Polymers52,6352
Non-polymers6033
Water79344
1
A: UbiD family decarboxylase
B: UNK
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)319,42930
Polymers315,80912
Non-polymers3,62018
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation4_555-y,-x,-z1
crystal symmetry operation5_655-x+y+1,y,-z1
crystal symmetry operation6_545x,x-y-1,-z1
Buried area31510 Å2
ΔGint-231 kcal/mol
Surface area98370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.696, 124.696, 68.846
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number149
Space group name H-MP312
Components on special symmetry positions
IDModelComponents
11B-3-

UNK

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein UbiD family decarboxylase


Mass: 52191.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium fortuitum (bacteria) / Gene: XA26_16650 / Production host: Escherichia (bacteria) / References: UniProt: A0A0N9Y7U2
#2: Protein/peptide UNK


Mass: 443.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: unidentified (others)

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Non-polymers , 4 types, 47 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-4LU / 1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-y l)-D-ribitol / prenylated-FMN iminium form


Mass: 525.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N4O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.94 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.06 M Divalents, 0.1 M Buffer System 2 pH 7.5, 30% Precipitant mix 3

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→58.42 Å / Num. obs: 25728 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 1 / Net I/σ(I): 16.6
Reflection shellResolution: 2.35→2.39 Å / Num. unique obs: 1284 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ABN

7abn


Resolution: 2.65→58.12 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.918 / SU B: 26.797 / SU ML: 0.259 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.678 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 866 4.8 %RANDOM
Rwork0.1844 ---
obs0.1881 16994 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 142.42 Å2 / Biso mean: 71.789 Å2 / Biso min: 35.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0.27 Å20 Å2
2---0.54 Å20 Å2
3---1.74 Å2
Refinement stepCycle: final / Resolution: 2.65→58.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3663 0 38 44 3745
Biso mean--73.29 65.23 -
Num. residues----482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123791
X-RAY DIFFRACTIONr_angle_refined_deg2.011.6375182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.535480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15521.064188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.27615576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4781530
X-RAY DIFFRACTIONr_chiral_restr0.1370.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022949
LS refinement shellResolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 63 -
Rwork0.281 1240 -
all-1303 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6769-0.2816-0.73570.24080.03971.8660.0313-0.18080.16380.0350.06840.2172-0.2269-0.4929-0.09970.4293-0.03080.1050.67170.06360.353918.784-40.27516.658
21.26560.11590.53161.8667-0.17221.70350.0741-0.03740.10490.03160.0280.2369-0.1554-0.2864-0.1020.2779-0.0060.01450.35940.02350.046641.605-36.064-1.036
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 318
2X-RAY DIFFRACTION1A454 - 999
3X-RAY DIFFRACTION2A319 - 453

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