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

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Basic information

Entry
Database: PDB / ID: 7jmr
TitleCrystal structure of the pea pathogenicity protein 2 from Madurella mycetomatis
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 / metal ion binding / : / Pea pathogenicity protein 2
Function and homology information
Biological speciesMadurella mycetomatis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.67 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 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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)27,8015
Polymers27,6411
Non-polymers1594
Water2,576143
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)83,40215
Polymers82,9243
Non-polymers47812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.853, 98.853, 62.380
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-478-

HOH

21A-533-

HOH

31A-537-

HOH

41A-540-

HOH

51A-541-

HOH

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Components

#1: Protein Pea pathogenicity protein 2


Mass: 27641.273 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-K / POTASSIUM ION


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


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.39 Å3/Da / Density % sol: 63.75 %
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: 1.67→38.74 Å / Num. obs: 78547 / % possible obs: 99.5 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 40
Reflection shellResolution: 1.67→1.69 Å / Num. unique obs: 2702 / Rsym value: 0.704 / % possible all: 96

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.67→38.74 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0.63 / Phase error: 19.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1955 3942 5.02 %
Rwork0.1773 74605 -
obs0.1782 78547 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.31 Å2 / Biso mean: 35.6067 Å2 / Biso min: 17.87 Å2
Refinement stepCycle: final / Resolution: 1.67→38.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 4 143 1960
Biso mean--41.59 36.8 -
Num. residues----224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011863
X-RAY DIFFRACTIONf_angle_d1.0292518
X-RAY DIFFRACTIONf_dihedral_angle_d6.869243
X-RAY DIFFRACTIONf_chiral_restr0.062256
X-RAY DIFFRACTIONf_plane_restr0.007323
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.67-1.690.37011350.29892567270296
1.69-1.710.29411640.271826802844100
1.71-1.740.2791520.248826662818100
1.74-1.760.29881180.240326392757100
1.76-1.780.26791260.227427132839100
1.78-1.810.23671760.218626212797100
1.81-1.840.28031340.202427082842100
1.84-1.870.21081420.202526722814100
1.87-1.90.22941440.194726992843100
1.9-1.940.1911380.189226992837100
1.94-1.970.2321530.194326212774100
1.97-2.010.20781060.184127682874100
2.01-2.060.2031560.179926332789100
2.06-2.110.19591360.187826412777100
2.11-2.160.20161760.179526822858100
2.16-2.220.20271500.18826452795100
2.22-2.280.19751300.176926862816100
2.28-2.360.19341480.172426632811100
2.36-2.440.19991520.177626912843100
2.44-2.540.1621300.170326912821100
2.54-2.650.20191380.170926642802100
2.65-2.790.16241400.176526592799100
2.79-2.970.17481140.175526872801100
2.97-3.20.19521390.18352694283399
3.2-3.520.20621530.17982627278099
3.52-4.030.169770.15472622269996
4.03-5.070.15851510.14542607275898
5.07-38.740.20791640.187826602824100

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