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- PDB-5ssy: Crystal Structure of human formylglycine generating enzyme -

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Basic information

Entry
Database: PDB / ID: 5ssy
TitleCrystal Structure of human formylglycine generating enzyme
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
Similarity search - Function
Sulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1 / Sulfatase-modifying factor enzyme superfamily / C-type lectin fold
Similarity search - Domain/homology
COPPER (I) ION / methyl N-acetyl-L-cysteinate / Formylglycine-generating enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 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 in complex with N-acetyl-cysteine methylester
Authors: Kowal, J. / Schlotawa, L. / Rudolph, M.G. / Niemann, H.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formylglycine-generating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6716
Polymers36,1291
Non-polymers5425
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.475, 61.731, 109.719
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-777-

HOH

21A-828-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 36128.930 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 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q8NBK3, formylglycine-generating enzyme
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 361 molecules

#2: Chemical ChemComp-CU1 / COPPER (I) ION / Copper


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: Chemical ChemComp-UG6 / methyl N-acetyl-L-cysteinate


Mass: 177.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.04 Å3/Da / Density % sol: 39.63 %
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: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→54.86 Å / Num. obs: 87450 / % possible obs: 93.8 % / Redundancy: 5.247 % / Biso Wilson estimate: 10.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.098 / Χ2: 1.024 / Net I/σ(I): 9.13 / Num. measured all: 458831 / Scaling rejects: 4407
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
1.2-1.231.881.2660.537660679440750.5391.66160
1.23-1.262.2910.9980.911799663551500.7071.2677.6
1.26-1.32.8581.2610.7916657645658290.6551.52890.3
1.3-1.344.1121.1581.0325506629962030.571.32998.5
1.34-1.395.3060.9411.8631703607059750.7991.04598.4
1.39-1.436.0530.7082.1935836592259200.8060.775100
1.43-1.495.9240.6443.0933289569956190.8710.70798.6
1.49-1.555.8910.4653.9731658550753740.9330.51297.6
1.55-1.625.9710.3075.0231532528252810.9470.337100
1.62-1.76.4450.2376.7832367502250220.9710.258100
1.7-1.796.6960.2038.6432156480548020.9790.2299.9
1.79-1.96.5370.15611.2529718459245460.9870.1799
1.9-2.035.7840.1214.7523090427939920.9890.13393.3
2.03-2.195.4460.09117.0821513403939500.9920.10297.8
2.19-2.45.6720.07121.1320540369036210.9940.0898.1
2.4-2.686.4080.06324.7721658339233800.9960.06999.6
2.68-3.16.3220.05228.3318839299029800.9980.05799.7
3.1-3.795.7420.04332.1514578256025390.9970.04899.2
3.79-5.365.6230.04134.5511230202519970.9970.04598.6
5.36-54.866.2780.03635.967502120011950.9980.03999.6

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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: inhouse model

Resolution: 1.29→54.86 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 6595 5.09 %RANDOM
Rwork0.2116 122908 --
obs0.2129 129503 89.22 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.31 Å2 / Biso mean: 15.3565 Å2 / Biso min: 5.16 Å2
Refinement stepCycle: final / Resolution: 1.29→54.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 39 357 2592
Biso mean--23.95 23.39 -
Num. residues----277
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 (%)
1.29-1.30.6395230.51264304539
1.3-1.320.3749460.39641113115924
1.32-1.330.33941050.29081856196141
1.33-1.350.2811860.29172801298761
1.35-1.370.38612030.35773691389480
1.37-1.380.50112310.4494010424189
1.38-1.40.27332240.25954637486199
1.4-1.430.23723000.25645094809100
1.43-1.450.3432700.34884547481799
1.45-1.470.33582230.341645904813100
1.47-1.50.28451990.29834602480199
1.5-1.520.40132670.3554456472398
1.52-1.550.30852220.25844569479199
1.55-1.590.20672350.188745754810100
1.59-1.620.20752280.180746154843100
1.62-1.660.21552220.181346214843100
1.66-1.70.20632130.174546074820100
1.7-1.740.22142660.191645924858100
1.74-1.80.212660.174646014867100
1.8-1.850.18012620.176245014763100
1.85-1.920.34762360.32164368460495
1.92-20.23152200.23774380460095
2-2.090.3542660.25234430469697
2.09-2.20.22952280.174550477899
2.2-2.340.26322360.2524387462395
2.34-2.520.21662500.182445954845100
2.52-2.770.18852090.188645854794100
2.77-3.170.2112610.171645834844100
3.17-3.990.16822710.15824516478799
3.99-54.860.16332270.146245914818100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4626-0.00830.27090.39970.26090.3193-0.01120.05550.0275-0.14220.0146-0.0188-0.09870.1085-00.121-0.00740.00550.07620.00180.081318.105680.300813.1323
20.48630.13140.18280.4056-0.15560.24-0.0410.0241-0.092-0.01240.03830.06720.07510.0158-0.00150.0683-0.00630.00350.08-0.00670.08466.787859.365121.0008
30.7555-0.0497-0.02370.6268-0.03660.3856-0.00190.0262-0.0492-0.00740.0066-0.03410.01640.00550.00050.05060.0016-0.00140.0457-0.00930.037217.641666.348619.3597
40.53110.15090.0180.14060.06170.5273-0.00510.13290.0697-0.2263-0.0202-0.0539-0.06550.0872-0.00030.1262-0.0015-0.01120.1033-0.00220.071216.728772.20557.8031
50.53820.06570.15390.6738-0.22040.2472-0.0306-0.03390.03720.0309-0.02690.1668-0.0606-0.1223-0.03070.07010.01760.00280.0794-0.00930.08877.271372.127220.7751
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 87 through 127 )A87 - 127
2X-RAY DIFFRACTION2chain 'A' and (resid 128 through 179 )A128 - 179
3X-RAY DIFFRACTION3chain 'A' and ((resid 180 through 309 ) or (resid 500))A0
4X-RAY DIFFRACTION4chain 'A' and ((resid 310 through 349 ) or (name CU))A0
5X-RAY DIFFRACTION5chain 'A' and (resid 350 through 375 )A350 - 375

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