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- PDB-8rl0: Crystal structure of a cysteine hydrolase from Ustilago maydis -

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Basic information

Entry
Database: PDB / ID: 8rl0
TitleCrystal structure of a cysteine hydrolase from Ustilago maydis
ComponentsIsochorismatase-like domain-containing protein
KeywordsHYDROLASE / Ustilago maydis / cysteine hydrolase / biotrophy
Function / homology: / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / Isochorismatase-like domain-containing protein
Function and homology information
Biological speciesUstilago maydis 521 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsAltegoer, F. / Christ, M. / Bange, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
Not funded Germany
CitationJournal: To Be Published
Title: Structural and functional characterization of an isochorismate (ISC)-like protein in a plant-pathogenic fungus
Authors: Rubio Elizalde, I. / Christ, M. / Weiland, P. / Jalomo, E. / Voll, L. / Altegoer, F. / Bange, G.
History
DepositionJan 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isochorismatase-like domain-containing protein


Theoretical massNumber of molelcules
Total (without water)24,2421
Polymers24,2421
Non-polymers00
Water79344
1
A: Isochorismatase-like domain-containing protein

A: Isochorismatase-like domain-containing protein

A: Isochorismatase-like domain-containing protein

A: Isochorismatase-like domain-containing protein


Theoretical massNumber of molelcules
Total (without water)96,9684
Polymers96,9684
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area8940 Å2
ΔGint-1 kcal/mol
Surface area29150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.250, 94.250, 40.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein Isochorismatase-like domain-containing protein


Mass: 24242.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ustilago maydis 521 (fungus) / Gene: UMAG_12021 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D1DWT4
#2: Water ChemComp-HOH / water


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

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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: 1.83 Å3/Da / Density % sol: 32.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 7.0, 20% PEG-2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.976253 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976253 Å / Relative weight: 1
ReflectionResolution: 1.81→42.15 Å / Num. obs: 16972 / % possible obs: 99.71 % / Redundancy: 11.9 % / Biso Wilson estimate: 33.31 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1354 / Net I/σ(I): 10.4
Reflection shellResolution: 1.81→1.875 Å / Rmerge(I) obs: 2.842 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 1623 / CC1/2: 0.695

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→42.15 Å / SU ML: 0.2467 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.4107
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2579 848 5 %
Rwork0.2172 16152 -
obs0.2192 16971 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.16 Å2
Refinement stepCycle: LAST / Resolution: 1.81→42.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1570 0 0 44 1614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621592
X-RAY DIFFRACTIONf_angle_d0.84242153
X-RAY DIFFRACTIONf_chiral_restr0.0534265
X-RAY DIFFRACTIONf_plane_restr0.006272
X-RAY DIFFRACTIONf_dihedral_angle_d6.032210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.920.4281340.43152550X-RAY DIFFRACTION96.79
1.92-2.070.38331390.33882651X-RAY DIFFRACTION99.93
2.07-2.280.30021400.27122664X-RAY DIFFRACTION99.93
2.28-2.610.2761410.23082680X-RAY DIFFRACTION99.93
2.61-3.280.28471440.22872727X-RAY DIFFRACTION99.9
3.28-42.150.2111520.17372880X-RAY DIFFRACTION99.9

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