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- PDB-2ifa: Crystal Structure of the PUTATIVE NITROREDUCTASE (SMU.260) IN COM... -

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Basic information

Entry
Database: PDB / ID: 2ifa
TitleCrystal Structure of the PUTATIVE NITROREDUCTASE (SMU.260) IN COMPLEX WITH FMN FROM STREPTOCOCCUS MUTANS, NORTHEAST STRUCTURAL GENOMICS TARGET SMR5.
ComponentsHypothetical protein SMU.260
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


cellular response to oxidative stress / oxidoreductase activity / nucleotide binding
Similarity search - Function
Nitroreductase Frm2/Hbn1-like / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Nitroreductase domain-containing protein
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsForouhar, F. / Chen, Y. / Xiao, R. / Ma, L.C. / Byler, T. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
History
DepositionSep 20, 2006Deposition site: RCSB / Processing site: RCSB
SupersessionOct 3, 2006ID: 1YW3
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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
A: Hypothetical protein SMU.260
B: Hypothetical protein SMU.260
C: Hypothetical protein SMU.260
D: Hypothetical protein SMU.260
E: Hypothetical protein SMU.260
F: Hypothetical protein SMU.260
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,71612
Polymers141,9786
Non-polymers2,7386
Water8,845491
1
A: Hypothetical protein SMU.260
B: Hypothetical protein SMU.260
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2394
Polymers47,3262
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-38 kcal/mol
Surface area17220 Å2
MethodPISA
2
C: Hypothetical protein SMU.260
D: Hypothetical protein SMU.260
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2394
Polymers47,3262
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-36 kcal/mol
Surface area17360 Å2
MethodPISA
3
E: Hypothetical protein SMU.260
F: Hypothetical protein SMU.260
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2394
Polymers47,3262
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-38 kcal/mol
Surface area17610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.435, 60.871, 109.155
Angle α, β, γ (deg.)90.00, 117.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hypothetical protein SMU.260


Mass: 23662.988 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: SMU.260 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8DW21
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 MM SODIUM ACETATE, 18% PEG3350, 240 MM AMMONIUM DIHYDROGEN PHOSPHATE, 10 MM FMN, AND 5 DTT., pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97894 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 8, 2005 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 2.3→29.03 Å / Num. all: 110600 / Num. obs: 106951 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.057 / Net I/σ(I): 17.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 5.2 / Num. unique all: 10679 / Rsym value: 0.203 / % possible all: 96.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
XTALVIEWrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.3→29.03 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 244508.83 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 9648 9.8 %RANDOM
Rwork0.218 ---
all0.22 110600 --
obs0.218 98879 89.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.4646 Å2 / ksol: 0.328468 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å25.73 Å2
2--1.17 Å20 Å2
3----1.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9511 0 186 491 10188
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 1404 9.5 %
Rwork0.221 13448 -
obs-13448 80.1 %

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