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- PDB-7jmv: Crystal structure of the pea pathogenicity protein 2 from Madurel... -

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Basic information

Entry
Database: PDB / ID: 7jmv
TitleCrystal structure of the pea pathogenicity protein 2 from Madurella mycetomatis complexed with 4-nitrocatechol
ComponentsPea pathogenicity protein 2
KeywordsLYASE / Gallic acid decarboxylase
Function / homologySnoaL-like domain / SnoaL-like domain / WW/rsp5/WWP domain profile. / WW domain / NTF2-like domain superfamily / 4-NITROCATECHOL / : / Pea pathogenicity protein 2
Function and homology information
Biological speciesMadurella mycetomatis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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
DepositionAug 3, 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

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Assembly

Deposited unit
A: Pea pathogenicity protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6815
Polymers27,4071
Non-polymers2744
Water2,936163
1
A: Pea pathogenicity protein 2
hetero molecules

A: Pea pathogenicity protein 2
hetero molecules

A: Pea pathogenicity protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,04315
Polymers82,2203
Non-polymers82312
Water543
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
MethodPISA
Unit cell
Length a, b, c (Å)98.740, 98.740, 62.287
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-302-

K

21A-451-

HOH

31A-533-

HOH

41A-555-

HOH

51A-560-

HOH

61A-561-

HOH

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Components

#1: Protein Pea pathogenicity protein 2


Mass: 27406.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Madurella mycetomatis (fungus) / Gene: MMYC01_201259, MMYC01_203104 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A175WC91
#2: Chemical ChemComp-4NC / 4-NITROCATECHOL


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


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.2 Å3/Da / Density % sol: 61.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 15 % PEG 3350, 0.2 M Calcium Chloride, 0.1 M MES / PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.57→42.76 Å / Num. obs: 49087 / % possible obs: 99.9 % / Redundancy: 9.8 % / Rsym value: 0.08 / Net I/σ(I): 41.4
Reflection shellResolution: 1.57→1.6 Å / Num. unique obs: 3019 / Rsym value: 0.894

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JMR

7jmr


Resolution: 1.57→42.76 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1907 2282 4.65 %
Rwork0.1766 46805 -
obs0.1772 49087 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.14 Å2 / Biso mean: 26.764 Å2 / Biso min: 8.58 Å2
Refinement stepCycle: final / Resolution: 1.57→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1805 0 19 163 1987
Biso mean--22.06 31.03 -
Num. residues----223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011866
X-RAY DIFFRACTIONf_angle_d1.0382522
X-RAY DIFFRACTIONf_dihedral_angle_d6.711242
X-RAY DIFFRACTIONf_chiral_restr0.061255
X-RAY DIFFRACTIONf_plane_restr0.007323
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.57-1.60.25861260.28322893301999
1.6-1.640.30751200.24629233043100
1.64-1.680.24121560.213728703026100
1.68-1.730.21141540.201228833037100
1.73-1.780.21621400.194628993039100
1.78-1.840.22121480.192928963044100
1.84-1.90.20421720.192928853057100
1.9-1.980.23111480.185929053053100
1.98-2.070.21971380.170229003038100
2.07-2.180.18491280.166929223050100
2.18-2.310.15221440.169329293073100
2.31-2.490.20651450.166829413086100
2.49-2.740.18771370.173429393076100
2.74-3.140.19321360.179129523088100
3.14-3.960.18121390.161329843123100
3.96-42.760.16271510.170130843235100

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