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- PDB-5ssx: Crystal Structure human formylglycine generating enzyme E130D mutant -

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Basic information

Entry
Database: PDB / ID: 5ssx
TitleCrystal Structure human formylglycine generating enzyme E130D mutant
ComponentsFormylglycine-generating enzyme
KeywordsOXIDOREDUCTASE / FORMYLGLYCINE / MULTIPLE SULFATASE DEFICIENCY / COPPER
Function / homology
Function and homology information


The activation of arylsulfatases / formylglycine-generating enzyme / formylglycine-generating oxidase activity / protein oxidation / glycosphingolipid catabolic process / Glycosphingolipid catabolism / cupric ion binding / post-translational protein modification / oxidoreductase activity / endoplasmic reticulum lumen ...The activation of arylsulfatases / formylglycine-generating enzyme / formylglycine-generating oxidase activity / protein oxidation / glycosphingolipid catabolic process / Glycosphingolipid catabolism / cupric ion binding / post-translational protein modification / oxidoreductase activity / endoplasmic reticulum lumen / endoplasmic reticulum / identical protein binding / membrane
Similarity search - Function
: / Sulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1-like domain / Sulfatase-modifying factor enzyme superfamily / C-type lectin fold
Similarity search - Domain/homology
COPPER (I) ION / Formylglycine-generating enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
AuthorsRadhakrishnan, K. / Schlotawa, L. / Rudolph, M.G.
Funding support Germany, 1items
OrganizationGrant numberCountry
University of Bielefeld Germany
CitationJournal: To be published
Title: Crystal Structure of human formylglycine generating enzyme E130D mutant
Authors: Kowal, J. / Schlotawa, L. / Niemann, H. / Rudolph, M.G.
History
DepositionAug 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_title
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Formylglycine-generating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6835
Polymers36,1151
Non-polymers5684
Water7,620423
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.494, 61.640, 109.579
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Formylglycine-generating enzyme / FGE / C-alpha-formylglycine-generating enzyme 1 / Sulfatase-modifying factor 1


Mass: 36114.902 Da / Num. of mol.: 1 / Mutation: E130D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMF1, PSEC0152, UNQ3037/PRO9852 / Plasmid: pAcGP67B-His7 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q8NBK3, formylglycine-generating enzyme
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#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.: 423 / Source method: isolated from a natural source / Formula: H2O
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: 2.03 Å3/Da / Density % sol: 39.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 9.6 mg/mL protein in 20mM Tris/HCl pH8.0 mixed 1:1 with reservoir 0.1M Tris/HCl pH 8.5, 20-25% PEG4000, 0.2-0.3M CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.02→40.95 Å / Num. obs: 142078 / % possible obs: 97.3 % / Redundancy: 5.487 % / Biso Wilson estimate: 8.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.057 / Χ2: 1.074 / Net I/σ(I): 14.49 / Num. measured all: 779553 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.02-1.061.8710.8420.89147641069678900.5261.08773.8
1.06-1.092.4130.6531.35228911044094860.6720.8290.9
1.09-1.123.4960.5322.3348611011899730.8120.62698.6
1.12-1.155.3910.4823.7152858982898050.8960.53399.8
1.15-1.195.8330.3665.0155785956695630.9470.401100
1.19-1.235.7480.2826.0253234926892610.9660.3199.9
1.23-1.286.1990.2227.4955497895389520.9780.242100
1.28-1.336.4220.1739.2155239860386020.9860.188100
1.33-1.396.2560.1410.9751654825882570.9890.152100
1.39-1.466.2260.11113.5549263791479130.9930.122100
1.46-1.546.6660.09417.0450305754875470.9950.102100
1.54-1.636.5870.07620.6346949713371280.9960.08399.9
1.63-1.746.1540.06623.4941549675467510.9970.072100
1.74-1.886.6660.05628.6741697625662550.9980.061100
1.88-2.066.5880.04932.9938270581258090.9980.05399.9
2.06-2.36.2070.04435.3332641526852590.9980.04899.8
2.3-2.665.9360.0436.6127752468046750.9980.04499.9
2.66-3.266.3440.03640.7325317399939910.9990.03999.8
3.26-4.615.7350.03241.2717875313131170.9990.03599.6
4.61-40.956.0480.0342.411152185518440.9990.03399.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1z70

1z70


Resolution: 1.02→40.95 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 12.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1375 12599 4.98 %RANDOM
Rwork0.123 240232 --
obs0.1238 252831 86.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.35 Å2 / Biso mean: 14.0685 Å2 / Biso min: 5.17 Å2
Refinement stepCycle: final / Resolution: 1.02→40.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2199 0 54 430 2683
Biso mean--36.74 24.37 -
Num. residues----278
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 (%)
1.02-1.030.2465230.25444474705
1.03-1.040.2396440.2567547988
1.04-1.050.2494790.27711436151516
1.05-1.070.29151650.28942868303331
1.07-1.080.30473350.31755640597561
1.08-1.090.30333820.29337860824285
1.09-1.110.25384490.26218837928694
1.11-1.130.25154540.2399022947698
1.13-1.140.22284750.20839283975899
1.14-1.160.18265100.17389097960799
1.16-1.180.17235080.16249219972799
1.18-1.210.18274800.15369198967899
1.21-1.230.1534590.14579227968699
1.23-1.250.13765030.14369260976399
1.25-1.280.15175210.138492619782100
1.28-1.310.14955180.135191849702100
1.31-1.340.13524920.111492239715100
1.34-1.380.12494350.102392599694100
1.38-1.420.11534110.097193559766100
1.42-1.470.10744450.091492479692100
1.47-1.520.10275100.086592709780100
1.52-1.580.09554870.083592749761100
1.58-1.650.10694580.083392769734100
1.65-1.740.10084730.086693079780100
1.74-1.850.10615110.091192149725100
1.85-1.990.10765050.095192659770100
1.99-2.190.11695050.100492469751100
2.19-2.510.1325210.11099170969199
2.51-3.160.13584750.127992699744100
3.16-40.950.15014660.133592649730100

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