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- PDB-4pu0: Crystal structure of the Escherichia coli alkanesulfonate FMN red... -

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Basic information

Entry
Database: PDB / ID: 4pu0
TitleCrystal structure of the Escherichia coli alkanesulfonate FMN reductase SsuE in FMNH2-bound form
ComponentsFMN reductase SsuE
KeywordsOXIDOREDUCTASE / Flavodoxin-like Fold / NADPH-dependent FMN reductase / SsuD
Function / homology
Function and homology information


FMN reductase complex / FMN reductase [NAD(P)H] activity / FMN reductase (NADPH) / cellular response to sulfate starvation / FMN reductase (NADPH) activity / alkanesulfonate catabolic process / DNA damage response / protein homodimerization activity
Similarity search - Function
NADPH-dependent FMN reductase, SsuE / : / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / FMN reductase (NADPH)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3018 Å
AuthorsDriggers, C.M. / Ellis, H.R. / Karplus, P.A.
CitationJournal: Biochemistry / Year: 2014
Title: Crystal Structure of Escherichia coli SsuE: Defining a General Catalytic Cycle for FMN Reductases of the Flavodoxin-like Superfamily.
Authors: Driggers, C.M. / Dayal, P.V. / Ellis, H.R. / Karplus, P.A.
History
DepositionMar 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: FMN reductase SsuE
A: FMN reductase SsuE
B: FMN reductase SsuE
D: FMN reductase SsuE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,94812
Polymers85,1134
Non-polymers1,8358
Water3,189177
1
C: FMN reductase SsuE
D: FMN reductase SsuE
hetero molecules

C: FMN reductase SsuE
D: FMN reductase SsuE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,49114
Polymers85,1134
Non-polymers2,37810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area8360 Å2
ΔGint-52 kcal/mol
Surface area25800 Å2
MethodPISA
2
A: FMN reductase SsuE
B: FMN reductase SsuE
hetero molecules

A: FMN reductase SsuE
B: FMN reductase SsuE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,40610
Polymers85,1134
Non-polymers1,2936
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area8580 Å2
ΔGint-48 kcal/mol
Surface area25830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.018, 187.018, 91.336
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein
FMN reductase SsuE / FMN reductase / Sulfate starvation-induced protein 4 / SSI4


Mass: 21278.271 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ssuE, ycbP, b0937, JW0920 / Production host: Escherichia coli (E. coli) / References: UniProt: P80644, FMN reductase (NADPH)
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: SsuE was concentrated to ~10 mg/mL in 10 mM HEPES, pH 7.0. Crystals were grown at room temperature using hanging drops made with the 4 l of protein stock mixed with 2 l of a reservoir ...Details: SsuE was concentrated to ~10 mg/mL in 10 mM HEPES, pH 7.0. Crystals were grown at room temperature using hanging drops made with the 4 l of protein stock mixed with 2 l of a reservoir containing 7.5% (w/v) polyethylene glycol (PEG) 3350 and 0.1 M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2010
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 42033 / Num. obs: 42033 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.3→2.34 Å / Mean I/σ(I) obs: 0.65 / % possible all: 98.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo SsuE

Resolution: 2.3018→46.755 Å / SU ML: 0.31 / σ(F): 1.35 / Phase error: 24.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 2118 5.1 %RANDOM (same as apo and FMN-bound SsuE)
Rwork0.1735 ---
obs0.176 41540 98.7 %-
all-42033 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3018→46.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5427 0 121 177 5725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135720
X-RAY DIFFRACTIONf_angle_d1.3937827
X-RAY DIFFRACTIONf_dihedral_angle_d14.7772043
X-RAY DIFFRACTIONf_chiral_restr0.076897
X-RAY DIFFRACTIONf_plane_restr0.008988
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3018-2.35540.39941310.32632323X-RAY DIFFRACTION89
2.3554-2.41430.32241410.26472469X-RAY DIFFRACTION95
2.4143-2.47960.29831440.23752561X-RAY DIFFRACTION98
2.4796-2.55250.29351170.20822614X-RAY DIFFRACTION100
2.5525-2.63490.22841420.19222639X-RAY DIFFRACTION100
2.6349-2.72910.28631410.19862597X-RAY DIFFRACTION100
2.7291-2.83830.25681260.19762666X-RAY DIFFRACTION100
2.8383-2.96750.26151430.20442634X-RAY DIFFRACTION100
2.9675-3.12390.29591440.19162645X-RAY DIFFRACTION100
3.1239-3.31960.2131540.17722633X-RAY DIFFRACTION100
3.3196-3.57580.23291470.16742653X-RAY DIFFRACTION100
3.5758-3.93550.19921560.16172664X-RAY DIFFRACTION100
3.9355-4.50450.16741520.13112684X-RAY DIFFRACTION100
4.5045-5.67370.20021400.1442739X-RAY DIFFRACTION100
5.6737-46.76410.20641400.18112901X-RAY DIFFRACTION100
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)
14.00380.218-0.56583.12090.55033.21670.0606-0.18550.06150.2945-0.06910.30360.2649-0.13280.00770.4343-0.0361-0.02360.3124-0.04780.4492105.123230.3098-5.9388
24.14890.04760.78574.1720.48132.88140.12730.4216-0.7111-0.05560.2765-0.37110.4710.6995-0.33990.51240.1256-0.130.5807-0.22990.5712129.864419.1904-16.2337
33.43960.04780.44753.2061-1.03293.5436-0.0562-0.0650.39910.22270.18150.3088-0.32060.0458-0.11020.4885-0.02110.01760.30.08250.443383.973514.02812.1945
43.9791-0.20650.30442.959-0.20363.5129-0.2193-0.42260.51490.29140.30490.6524-0.4917-0.4766-0.08210.63930.15970.16650.58750.22140.991856.80427.493912.0527
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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