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- PDB-5ssz: Crystal Structure of wild-type human formylglycine generating enz... -

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Basic information

Entry
Database: PDB / ID: 5ssz
TitleCrystal Structure of wild-type human formylglycine generating enzyme bound to Cu(I)
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 wild-type human formylglycine generating enzyme bound to Cu(I)
Authors: Radhakrishnan, K. / Schlotawa, L. / 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 1.2Nov 6, 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)36,4945
Polymers36,1291
Non-polymers3654
Water7,746430
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)43.513, 62.024, 110.021
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: 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
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#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


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
#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.: 430 / 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: 2.05 Å3/Da / Density % sol: 40.14 %
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: 0.99976 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99976 Å / Relative weight: 1
ReflectionResolution: 1→55.01 Å / Num. obs: 143525 / % possible obs: 89.4 % / Redundancy: 5.868 % / Biso Wilson estimate: 8.37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.04 / Χ2: 1.083 / Net I/σ(I): 21.76 / Num. measured all: 842259 / Scaling rejects: 28
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
1-1.031.6540.3311.4753431176332300.7870.43827.5
1.03-1.061.8910.2672.11121791143964410.8730.34256.3
1.06-1.092.310.2233.01202321116087600.9240.27478.5
1.09-1.123.1560.2064.8313411082299310.9410.24391.8
1.12-1.165.0860.1548.195295910498104120.9820.17299.2
1.16-1.26.6320.13311.246704710160101100.990.14599.5
1.2-1.246.5530.11812.564711988798750.9920.12999.9
1.24-1.296.6270.10314.562410941894170.9940.112100
1.29-1.357.0850.08817.7864493910691030.9960.095100
1.35-1.426.9560.07620.760346867886750.9960.082100
1.42-1.496.8390.06624.3956635828482810.9970.071100
1.49-1.587.2610.05629.957021785578530.9980.061100
1.58-1.697.1380.04933.9952789739773950.9980.053100
1.69-1.836.6580.04337.0745983691069060.9990.04799.9
1.83-27.2810.03843.1546419637663750.9990.041100
2-2.247.0450.03546.240675577657740.9990.037100
2.24-2.596.4380.0324633093514851400.9990.03599.8
2.59-3.177.20.02951.5331545438243810.9990.032100
3.17-4.486.7670.02751.5623366345534530.9990.02999.9
4.48-55.016.7920.02651.6913672201920130.9990.02899.7

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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: 1.02→55.01 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 11.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1417 13236 5.05 %RANDOM
Rwork0.1307 248714 --
obs0.1313 261950 88.88 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.45 Å2 / Biso mean: 12.4298 Å2 / Biso min: 5.48 Å2
Refinement stepCycle: final / Resolution: 1.02→55.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 17 430 2651
Biso mean--18.86 20.35 -
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 (%)
1.02-1.030.2711290.30162296242525
1.03-1.040.28751880.26583271345935
1.04-1.050.26932510.24894304455546
1.05-1.070.24052960.21995240553656
1.07-1.080.23852800.2036120640066
1.08-1.10.22563090.21786732704172
1.1-1.110.16574140.14857682809682
1.11-1.130.14294890.12778554904392
1.13-1.150.12385000.10959153965398
1.15-1.170.11124780.09939253973199
1.17-1.190.11995600.10199197975799
1.19-1.210.11954770.10292979774100
1.21-1.230.12615200.1059172969299
1.23-1.260.11925040.10993109814100
1.26-1.280.11945160.107593339849100
1.28-1.310.12654940.107392859779100
1.31-1.350.12224940.10293169810100
1.35-1.380.12135130.102292869799100
1.38-1.420.12064960.100393159811100
1.42-1.470.11454780.099993129790100
1.47-1.520.11244910.10293439834100
1.52-1.580.12324490.102593659814100
1.58-1.650.12155350.106292669801100
1.65-1.740.12674650.117793659830100
1.74-1.850.14155020.124893119813100
1.85-1.990.14685100.129493249834100
1.99-2.190.13324940.133193069800100
2.19-2.510.1514720.148293099781100
2.51-3.160.16394620.162193609822100
3.16-55.010.1574700.145593379807100

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