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

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Basic information

Entry
Database: PDB / ID: 4pty
TitleCrystal structure of the Escherichia coli alkanesulfonate FMN reductase SsuE in apo 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
PHOSPHATE ION / FMN reductase (NADPH)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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)85,76311
Polymers85,1134
Non-polymers6507
Water4,954275
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)85,66610
Polymers85,1134
Non-polymers5536
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area10660 Å2
ΔGint-43 kcal/mol
Surface area25630 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)85,86112
Polymers85,1134
Non-polymers7488
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area11060 Å2
ΔGint-76 kcal/mol
Surface area25350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.838, 185.838, 91.582
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.68 Å3/Da / Density % sol: 54.14 %
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: Apr 9, 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: 2.1→50 Å / Num. all: 54613 / Num. obs: 52483 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 0.36 / Num. unique all: 1922 / % possible all: 71.1

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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: pdb entry 2VZF

2vzf
PDB Unreleased entry


Resolution: 2.1→46.459 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 25.86 / Stereochemistry target values: CDL
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 2651 5.12 %RANDOM (same as FMN-bound and FMNH2-bound SsuE)
Rwork0.1795 ---
obs0.1821 51749 94.79 %-
all-52483 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→46.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5466 0 40 275 5781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145631
X-RAY DIFFRACTIONf_angle_d1.4117677
X-RAY DIFFRACTIONf_dihedral_angle_d15.0192028
X-RAY DIFFRACTIONf_chiral_restr0.076887
X-RAY DIFFRACTIONf_plane_restr0.008979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13820.3666750.33161588X-RAY DIFFRACTION58
2.1382-2.17940.36321100.3012022X-RAY DIFFRACTION76
2.1794-2.22380.30841290.29352258X-RAY DIFFRACTION85
2.2238-2.27220.34351320.28762475X-RAY DIFFRACTION92
2.2722-2.3250.33321470.26732568X-RAY DIFFRACTION96
2.325-2.38320.27081580.2442610X-RAY DIFFRACTION98
2.3832-2.44760.3061520.23222661X-RAY DIFFRACTION99
2.4476-2.51960.29251280.22132687X-RAY DIFFRACTION99
2.5196-2.6010.28211490.19912674X-RAY DIFFRACTION100
2.601-2.69390.25261390.1972716X-RAY DIFFRACTION99
2.6939-2.80180.3011290.19542687X-RAY DIFFRACTION99
2.8018-2.92920.2351370.18462710X-RAY DIFFRACTION100
2.9292-3.08370.26471450.19012718X-RAY DIFFRACTION100
3.0837-3.27680.24041690.17582716X-RAY DIFFRACTION100
3.2768-3.52970.23161520.16242718X-RAY DIFFRACTION100
3.5297-3.88480.21781550.15512737X-RAY DIFFRACTION100
3.8848-4.44650.16731560.13142758X-RAY DIFFRACTION100
4.4465-5.60060.18871420.14232820X-RAY DIFFRACTION100
5.6006-46.47080.21331470.19472975X-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)
13.06860.2249-0.44442.35380.00492.3897-0.0088-0.0705-0.0570.33070.03440.17460.179-0.1048-0.0260.3881-0.0869-0.00590.2031-0.02960.272104.192430.3665-6.0908
23.61050.17080.42193.24890.49072.38050.02920.6222-0.7474-0.06070.309-0.52620.45950.5704-0.28340.51660.0642-0.09040.5451-0.31290.567129.210419.0151-16.2372
33.03590.45910.35283.4338-1.02912.45070.0815-0.10990.27860.37830.0660.2855-0.2642-0.0465-0.12680.432-0.00410.08440.2080.07910.350482.959814.27842.3496
44.23540.0168-0.45283.79230.81534.04880.0992-0.72560.34820.4667-0.03590.8951-0.3575-0.625-0.06880.55480.07920.20710.68010.21220.900656.07198.411.9244
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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