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- PDB-6w2o: Crystal structure of uroporphyrinogen III decarboxylate (hemE) fr... -

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Basic information

Entry
Database: PDB / ID: 6w2o
TitleCrystal structure of uroporphyrinogen III decarboxylate (hemE) from Stenotrophomonas maltophilia
ComponentsUroporphyrinogen decarboxylase
KeywordsLYASE / National Institute of Allergy and Infectious Diseases / NIAID / aerobic nonfermentative Gram-negative bacterium / heme biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


uroporphyrinogen decarboxylase / uroporphyrinogen decarboxylase activity / protoporphyrinogen IX biosynthetic process / cytoplasm
Similarity search - Function
Uroporphyrinogen decarboxylase HemE / Uroporphyrinogen decarboxylase signature 1. / Uroporphyrinogen decarboxylase signature 2. / Uroporphyrinogen decarboxylase (URO-D) / Uroporphyrinogen decarboxylase (URO-D) / TIM Barrel - #210 / UROD/MetE-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Uroporphyrinogen decarboxylase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of uroporphyrinogen III decarboxylate (hemE) from Stenotrophomonas maltophilia
Authors: Edwards, T.E. / Davies, D.R. / Horanyi, P.S. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMar 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uroporphyrinogen decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6149
Polymers40,0351
Non-polymers5798
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.690, 103.690, 74.720
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Uroporphyrinogen decarboxylase / URO-D


Mass: 40034.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: hemE, Smlt3622 / Production host: Escherichia coli (E. coli) / References: UniProt: B2FQJ0, uroporphyrinogen decarboxylase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.9 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: StmaA.01152.a.B1.PW38744 at 20.4 mg/mL against JCSG+ condition G11: 0.1 M BisTris pH 5.5, 2.0 M ammonium sulfate, supplemented with 20% ethylene glycol as cryo-protectant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.55→44.9 Å / Num. obs: 67246 / % possible obs: 99.7 % / Redundancy: 5.457 % / Biso Wilson estimate: 27.608 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.066 / Χ2: 1.053 / Net I/σ(I): 14.21 / Num. measured all: 366930 / Scaling rejects: 4
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
1.55-1.595.5470.5273.1527501496049580.8840.582100
1.59-1.635.5410.4213.9326635480748070.9180.466100
1.63-1.685.5780.3374.8426128468546840.9440.372100
1.68-1.735.5810.2755.9525409455545530.9590.305100
1.73-1.795.5660.2187.3824596441944190.9720.242100
1.79-1.855.5630.1818.923889429642940.980.2100
1.85-1.925.5630.13911.1722746409440890.9870.15599.9
1.92-25.5470.11713.0822166399739960.9910.13100
2-2.095.4820.09615.4120798380237940.9910.10799.8
2.09-2.195.4470.08217.919854365636450.9930.09299.7
2.19-2.315.3830.07419.418645347334640.9940.08299.7
2.31-2.455.3880.06720.9917742331032930.9940.07599.5
2.45-2.625.3470.06322.5116479309030820.9940.0799.7
2.62-2.835.2950.05724.0315277290128850.9950.06499.4
2.83-3.15.2880.05325.1814028267226530.9960.05999.3
3.1-3.475.2260.0526.5812653243724210.9960.05699.3
3.47-45.2510.04627.5411274216221470.9970.05199.3
4-4.95.270.0428.29639183518290.9980.04599.7
4.9-6.935.280.03628.187582144314360.9980.0499.5
6.93-44.94.880.03227.2538898337970.9980.03695.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.18rc2refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wsh

4wsh


Resolution: 1.55→44.9 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.21
RfactorNum. reflection% reflection
Rfree0.1714 3920 6.04 %
Rwork0.1541 --
obs0.1551 64910 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.07 Å2 / Biso mean: 25.7342 Å2 / Biso min: 12 Å2
Refinement stepCycle: final / Resolution: 1.55→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2699 0 30 470 3199
Biso mean--68.89 38.74 -
Num. residues----355
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.570.24661120.19592037214989
1.57-1.590.20481260.18951992211889
1.59-1.610.19011350.17812057219292
1.61-1.630.20731480.17322073222192
1.63-1.660.17571280.17212032216091
1.66-1.680.22031280.16722097222593
1.68-1.710.20811350.1632092222793
1.71-1.730.19331240.16532129225395
1.73-1.760.20241570.15672124228195
1.76-1.80.17721240.1642134225895
1.8-1.830.17571310.16722150228196
1.83-1.870.15931330.15792167230096
1.87-1.910.18771480.16072184233297
1.91-1.950.19471460.16892186233298
1.95-20.17811410.15742204234598
2-2.060.17811550.15472177233298
2.06-2.120.17841290.15922233236298
2.12-2.180.17091540.15042215236999
2.18-2.260.17111270.15272253238099
2.26-2.350.17941350.14882227236299
2.35-2.460.19331400.15732270241099
2.46-2.590.17141700.16162220239099
2.59-2.750.18281430.15132247239099
2.75-2.960.16411610.15982255241699
2.97-3.260.18841540.15432266242099
3.26-3.730.13131310.13842294242599
3.74-4.70.13881450.126523102455100
4.71-44.90.1721600.16952365252598
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)
10.6070.1245-0.75430.9158-0.45631.1566-0.0284-0.07040.05950.00720.0092-0.0670.00170.13510.03030.1049-0.0055-0.02370.1593-0.00420.1152-1.4483-48.62946.6697
21.5199-0.7968-0.08761.4798-0.10140.8892-0.0422-0.12260.0910.05570.087-0.0178-0.09380.0907-0.04330.1498-0.0042-0.02560.1752-0.02610.1269-10.1191-37.34916.6972
30.94290.02460.18091.66970.7531.57710.04-0.04670.2069-0.0412-0.049-0.0434-0.15520.05920.00920.1174-0.02090.00440.1451-0.00170.17171.1105-33.7082-4.5877
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 92 )A3 - 92
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 262 )A93 - 262
3X-RAY DIFFRACTION3chain 'A' and (resid 263 through 357 )A263 - 357

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