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- PDB-2hay: The Crystal Structure of the Putative NAD(P)H-Flavin Oxidoreducta... -

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Basic information

Entry
Database: PDB / ID: 2hay
TitleThe Crystal Structure of the Putative NAD(P)H-Flavin Oxidoreductase from Streptococcus pyogenes M1 GAS
ComponentsPutative NAD(P)H-flavin oxidoreductase
KeywordsOXIDOREDUCTASE / alpha-beta structure / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor / 2,4,6-trinitrotoluene catabolic process / nucleotide binding / cytosol
Similarity search - Function
Oxygen-insensitive NAD(P)H nitroreductase NfsB-like / : / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NAD(P)H-flavin oxidoreductase
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.11 Å
AuthorsKim, Y. / Duggan, E. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2006
Title: The Crystal Structure of the Putative NAD(P)H-Flavin Oxidoreductase from Streptococcus pyogenes M1 GAS
Authors: Kim, Y. / Duggan, E. / Clancy, S. / Joachimiak, A.
History
DepositionJun 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: Putative NAD(P)H-flavin oxidoreductase
B: Putative NAD(P)H-flavin oxidoreductase
C: Putative NAD(P)H-flavin oxidoreductase
D: Putative NAD(P)H-flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,25213
Polymers103,9474
Non-polymers2,3069
Water10,971609
1
A: Putative NAD(P)H-flavin oxidoreductase
B: Putative NAD(P)H-flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1747
Polymers51,9732
Non-polymers1,2015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10080 Å2
ΔGint-101 kcal/mol
Surface area18130 Å2
MethodPISA
2
C: Putative NAD(P)H-flavin oxidoreductase
D: Putative NAD(P)H-flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0786
Polymers51,9732
Non-polymers1,1054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-94 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.205, 91.874, 175.693
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative NAD(P)H-flavin oxidoreductase / NADP / H-dependent quinone reductase


Mass: 25986.631 Da / Num. of mol.: 4 / Fragment: putative NAD(P)H-flavin oxidoreductase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Species: Streptococcus pyogenes / Strain: SF370 / Plasmid: pMCSG19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q9A120, Oxidoreductases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 609 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium Sulfate 0.1M MES pH 6.5 30% PEG 5000 MME and Flavin, VAPOR DIFFUSION, SITTING DROP, temperature 282K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2006 / Details: mirrors
RadiationMonochromator: double crystal monochromator Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. all: 58066 / Num. obs: 55236 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 9.2
Reflection shellResolution: 2.11→2.19 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.04 / % possible all: 73.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.11→40.71 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.133 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.264 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23246 5552 10.1 %RANDOM
Rwork0.17456 ---
all0.18034 49579 --
obs0.18034 49579 96.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.724 Å2
Baniso -1Baniso -2Baniso -3
1-3.6 Å20 Å20 Å2
2---1.97 Å20 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.11→40.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7049 0 149 609 7807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227656
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.98110389
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.985930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84724.197355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.873151414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6631548
X-RAY DIFFRACTIONr_chiral_restr0.1090.21106
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025752
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.23730
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2622
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6841.54542
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23927340
X-RAY DIFFRACTIONr_scbond_it2.03333114
X-RAY DIFFRACTIONr_scangle_it3.1454.53049
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.165 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.303 338
Rwork0.197 2845
obs-2845
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)
10.7603-0.140.141.0934-0.33772.33230.0001-0.0177-0.05050.08430.04860.03490.1038-0.2024-0.0487-0.04560.00880.031-0.12550.0126-0.094450.35830.9868.715
20.4954-0.0514-0.08140.82840.31412.60820.02540.0190.01360.01740.0417-0.0087-0.277-0.0556-0.0671-0.00980.04860.0319-0.14770.0197-0.099552.02444.26165.029
30.63820.0135-0.23721.4147-0.15872.53490.019-0.01260.1007-0.06130.0204-0.014-0.1602-0.0533-0.0394-0.0375-0.0364-0.0023-0.1455-0.0201-0.088747.6560.684109.797
40.66870.06080.00941.23480.40982.29250.0505-0.06390.01230.03370.0282-0.11110.09540.0854-0.0787-0.0591-0.03810.0027-0.1239-0.0063-0.101252.00248.224113.623
50.012-0.0998-0.05280.84890.58851.38940.35150.04940.09790.0212-0.0438-0.26230.01150.0385-0.3078-0.0245-0.04340.0793-0.0154-0.0205-0.07250.78446.06289.367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 221
2X-RAY DIFFRACTION2B1 - 221
3X-RAY DIFFRACTION3C4 - 221
4X-RAY DIFFRACTION4D0 - 221
5X-RAY DIFFRACTION5A702
6X-RAY DIFFRACTION5C704
7X-RAY DIFFRACTION5B701
8X-RAY DIFFRACTION5D703

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