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- PDB-8aru: Crystal Structure of human formylglycine generating enzyme -

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Basic information

Entry
Database: PDB / ID: 8aru
TitleCrystal Structure of human formylglycine generating enzyme
ComponentsFormylglycine-generating enzyme
KeywordsOXIDOREDUCTASE / FORMYLGLYCINE / MULTIPLE SULFATASE DEFICIENCY / MSD MUTATION
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
Formylglycine-generating enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsNeumann, P. / Dickmanns, A. / Ficner, R. / Rudolph, M.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Crystal Structure of human formylglycine generating enzyme E130A mutant
Authors: Kowal, J. / Neumann, P. / Dickmanns, A. / Ficner, R. / Schlotawa, L. / Niemann, H. / Schlotawa, L. / Rudolph, M.G.
History
DepositionAug 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)36,5754
Polymers36,0711
Non-polymers5053
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-20 kcal/mol
Surface area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.497, 61.562, 109.330
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: 36070.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMF1, PSEC0152, UNQ3037/PRO9852 / Plasmid: pAcGP67B-His7 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5
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-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 39.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 7-8 mg/mL protein in 20mM Tris/HCl pH8.0 mixed 1:1 with reservoir 0.1M Tris/HCl pH 8-9, 20-25% PEG4000, 0.25M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.92 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.08→43.5 Å / Num. obs: 114914 / % possible obs: 98.5 % / Redundancy: 4.089 % / Biso Wilson estimate: 6.58 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.107 / Χ2: 0.852 / Net I/σ(I): 10.12
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
1.11-1.142.2031.2210.6916292850773960.3321.53786.9
1.14-1.172.6441.0140.9521011827379470.4411.23596.1
1.17-1.23.4950.9041.3128294811780960.5451.06399.7
1.2-1.244.3320.8131.734241791179050.6020.92999.9
1.24-1.284.3760.6842.0433370763176250.6520.78299.9
1.28-1.334.3910.5932.3932233734673400.7120.67899.9
1.33-1.384.410.4762.9331331710971040.8040.54499.9
1.38-1.434.430.3873.6630443688368720.8470.44299.8
1.43-1.54.4590.2994.7629554663866280.8960.34199.8
1.5-1.574.440.2166.4528041631963150.9490.24799.9
1.57-1.654.4720.1698.3126789599859900.9640.19399.9
1.65-1.764.4750.12710.8825586572557170.9790.14599.9
1.76-1.884.4740.09514.3823895534853410.9880.10899.9
1.88-2.034.4710.06619.7522471503250260.9950.07699.9
2.03-2.224.4490.05125.2620623464146350.9970.05899.9
2.22-2.484.4430.04329.5218575420241810.9970.04999.5
2.48-2.874.4250.03534.0116478374137240.9980.0499.5
2.87-3.514.3930.02741.6113885319231610.9990.0399
3.51-4.964.3710.02248.8710854252924830.9990.02598.2
4.96-40.884.1250.02146.65890149414280.9990.02395.6

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Processing

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

1z70


Resolution: 1.08→40.88 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1736 4571 5.03 %RANDOM
Rwork0.1403 86289 --
obs0.142 90860 72.21 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.5 Å2 / Biso mean: 12.7678 Å2 / Biso min: 3.18 Å2
Refinement stepCycle: final / Resolution: 1.08→40.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 30 419 2649
Biso mean--31.95 25.65 -
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 (%)
1.08-1.090.617120.239852541
1.09-1.110.447790.2552002095
1.11-1.120.2563170.25293323498
1.12-1.130.216310.239850553613
1.13-1.150.2409390.22870073918
1.15-1.170.2412560.2235944100024
1.17-1.180.2956880.22751264135233
1.18-1.20.2666920.19991533162539
1.2-1.220.21311100.19351872198247
1.22-1.240.23821040.20652352245659
1.24-1.260.23671650.20552787295272
1.26-1.280.24771610.19653122328378
1.28-1.310.2361740.18963232340682
1.31-1.330.25271680.18623444361287
1.33-1.360.22372190.18413808402796
1.36-1.390.24652180.175939234141100
1.39-1.430.24642150.167139484163100
1.43-1.470.17241940.147439854179100
1.47-1.510.19422140.132739784192100
1.51-1.560.17481840.12439704154100
1.56-1.620.1632090.120440064215100
1.62-1.680.15882230.119939624185100
1.68-1.760.13931970.121440054202100
1.76-1.850.16932150.120339744189100
1.85-1.970.13562240.117739914215100
1.97-2.120.1421980.114840254223100
2.12-2.330.14832240.12140294253100
2.33-2.670.15032120.135540554267100
2.67-3.360.16011990.13394090428999
3.36-40.880.14622100.13034201441198

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