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

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Basic information

Entry
Database: PDB / ID: 4ptz
TitleCrystal structure of the Escherichia coli alkanesulfonate FMN reductase SsuE in FMN-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 (NADPH) / FMN reductase (NAD(P)H) activity / 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: 1.9007 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)89,13920
Polymers85,1134
Non-polymers4,02616
Water6,846380
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)88,58818
Polymers85,1134
Non-polymers3,47514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area8360 Å2
ΔGint-51 kcal/mol
Surface area26340 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)89,69122
Polymers85,1134
Non-polymers4,57718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area8320 Å2
ΔGint-48 kcal/mol
Surface area26150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.746, 186.746, 93.371
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.: 7 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.76 Å3/Da / Density % sol: 55.45 %
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: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2009
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 75282 / Num. obs: 75282 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 0.6 / % possible all: 100

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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: 1.9007→46.687 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 22.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 3848 5.14 %RANDOM (same as apo and FMNH2-bound SsuE)
Rwork0.1732 ---
obs0.175 74934 99.4 %-
all-75282 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9007→46.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5456 0 270 380 6106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125883
X-RAY DIFFRACTIONf_angle_d1.3868053
X-RAY DIFFRACTIONf_dihedral_angle_d16.2882098
X-RAY DIFFRACTIONf_chiral_restr0.077910
X-RAY DIFFRACTIONf_plane_restr0.007996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9007-1.92470.43751300.41642433X-RAY DIFFRACTION93
1.9247-1.950.41171450.372614X-RAY DIFFRACTION99
1.95-1.97680.30941280.30282587X-RAY DIFFRACTION100
1.9768-2.0050.32651610.27312610X-RAY DIFFRACTION100
2.005-2.03490.2871230.27032610X-RAY DIFFRACTION100
2.0349-2.06670.28881490.24172640X-RAY DIFFRACTION100
2.0667-2.10060.28381470.22832576X-RAY DIFFRACTION100
2.1006-2.13680.2711280.21642601X-RAY DIFFRACTION100
2.1368-2.17570.25321400.20812641X-RAY DIFFRACTION100
2.1757-2.21750.28711430.20772625X-RAY DIFFRACTION100
2.2175-2.26280.23851440.20552583X-RAY DIFFRACTION100
2.2628-2.3120.24391620.19072583X-RAY DIFFRACTION100
2.312-2.36580.20671300.18522630X-RAY DIFFRACTION100
2.3658-2.42490.23461670.18812602X-RAY DIFFRACTION100
2.4249-2.49050.26841490.18982612X-RAY DIFFRACTION100
2.4905-2.56380.23621240.17192607X-RAY DIFFRACTION99
2.5638-2.64650.21361380.17062656X-RAY DIFFRACTION99
2.6465-2.74110.19111400.1662619X-RAY DIFFRACTION99
2.7411-2.85080.24421310.17472638X-RAY DIFFRACTION99
2.8508-2.98060.21261340.17472630X-RAY DIFFRACTION100
2.9806-3.13770.22961380.16552653X-RAY DIFFRACTION100
3.1377-3.33420.181690.15642655X-RAY DIFFRACTION99
3.3342-3.59150.17941430.15032677X-RAY DIFFRACTION100
3.5915-3.95280.19211550.14552651X-RAY DIFFRACTION100
3.9528-4.52440.1391510.12582689X-RAY DIFFRACTION100
4.5244-5.69860.161380.14632753X-RAY DIFFRACTION100
5.6986-46.70060.22671410.18832911X-RAY DIFFRACTION99
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)
11.84510.398-0.04562.35040.35632.10540.0519-0.0156-0.03130.23810.00620.18990.39110.0005-0.05140.3964-0.0336-0.01970.1706-0.04510.3009105.197230.1644-6.2663
22.76940.86310.29343.2130.85122.6782-0.07490.4125-0.43380.16080.5027-0.54470.75140.8075-0.23230.52710.2202-0.12730.6436-0.33680.5016129.206920.2429-17.6782
31.85030.1351-0.09042.7512-0.85532.0686-0.0201-0.16540.15370.28880.10330.079-0.25740.0568-0.07660.47480.00820.01620.19140.03860.330683.861313.99712.1775
42.8651-0.16720.28253.5618-1.29712.7062-0.3054-0.24360.34120.89130.64620.6066-1.0946-1.0127-0.22460.97540.35370.1290.60480.25780.640856.64177.266712.2703
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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