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- PDB-2gsw: Crystal Structure of the Putative NADPH-dependent Azobenzene FMN-... -

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Basic information

Entry
Database: PDB / ID: 2gsw
TitleCrystal Structure of the Putative NADPH-dependent Azobenzene FMN-Reductase YhdA from Bacillus subtilis, Northeast Structural Genomics Target SR135
ComponentsyhdA
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / FMN binding / oxidoreductase activity / identical protein binding / cytosol
Similarity search - Function
: / 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 / : / FMN-dependent NADPH-azoreductase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.92 Å
AuthorsForouhar, F. / Hussain, M. / Jayaraman, S. / Shen, J. / Cooper, B. / Cunningham, K. / Janjua, H. / Ma, L.-C. / Xiao, R. / Acton, T.B. ...Forouhar, F. / Hussain, M. / Jayaraman, S. / Shen, J. / Cooper, B. / Cunningham, K. / Janjua, H. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Putative NADPH-dependent Azobenzene FMN-Reductase YhdA from Bacillus subtilis, Northeast Structural Genomics Target SR135
Authors: Forouhar, F. / Hussain, M. / Jayaraman, S. / Shen, J. / Cooper, B. / Cunningham, K. / Janjua, H. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionApr 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2024Group: 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

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Assembly

Deposited unit
A: yhdA
B: yhdA
C: yhdA
D: yhdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9398
Polymers81,1144
Non-polymers1,8254
Water77543
1
A: yhdA
C: yhdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4694
Polymers40,5572
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-28.2 kcal/mol
Surface area14080 Å2
MethodPISA
2
B: yhdA
D: yhdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4694
Polymers40,5572
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-27.4 kcal/mol
Surface area14250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.444, 99.296, 69.436
Angle α, β, γ (deg.)90.00, 103.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
yhdA


Mass: 20278.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Species: Bacillus subtilis / Strain: 168 / Gene: yhdA / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: GenBank: 2633257, UniProt: O07529*PLUS
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100mM Tris, 22% PEG3350, 180mM MgCl2, 5 mM NADPH, 5 mM DTT, pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97896, 0.97942, 0.96780
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 2006 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978961
20.979421
30.96781
ReflectionResolution: 2.9→29.72 Å / Num. all: 29319 / Num. obs: 28615 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 104.2 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.072 / Net I/σ(I): 14.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.92 / Num. unique all: 2904 / Rsym value: 0.326 / % possible all: 91.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
SOLVEphasing
RESOLVEphasing
XTALVIEWrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.92→29.72 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 372905.67 / 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
Rfree0.291 2392 9.6 %RANDOM
Rwork0.26 ---
all0.262 29319 --
obs0.26 25036 84.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.4155 Å2 / ksol: 0.291943 e/Å3
Displacement parametersBiso mean: 58.5 Å2
Baniso -1Baniso -2Baniso -3
1-7.06 Å20 Å26.08 Å2
2---10.09 Å20 Å2
3---3.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.92→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5140 0 124 43 5307
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.92→3.08 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 269 10.6 %
Rwork0.335 2263 -
obs-2263 50.2 %

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