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- PDB-4eh1: Crystal Structure of the Flavohem-like-FAD/NAD Binding Domain of ... -

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Basic information

Entry
Database: PDB / ID: 4eh1
TitleCrystal Structure of the Flavohem-like-FAD/NAD Binding Domain of Nitric Oxide Dioxygenase from Vibrio cholerae O1 biovar El Tor
ComponentsFlavohemoprotein
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta-alpha sandwich / beta structure
Function / homology
Function and homology information


nitric oxide dioxygenase / 6,7-dihydropteridine reductase activity / nitric oxide dioxygenase NAD(P)H activity / cellular response to nitrosative stress / nitric oxide catabolic process / FAD binding / oxygen carrier activity / response to toxic substance / oxygen binding / intracellular iron ion homeostasis ...nitric oxide dioxygenase / 6,7-dihydropteridine reductase activity / nitric oxide dioxygenase NAD(P)H activity / cellular response to nitrosative stress / nitric oxide catabolic process / FAD binding / oxygen carrier activity / response to toxic substance / oxygen binding / intracellular iron ion homeostasis / heme binding / metal ion binding
Similarity search - Function
Flavohemoprotein / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Globin/Protoglobin / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain ...Flavohemoprotein / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Globin/Protoglobin / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Globin domain profile. / Globin / Globin / Globin-like superfamily / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Flavohemoprotein
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKim, Y. / Gu, M. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of the Flavohem-like-FAD/NAD Binding Domain of Nitric Oxide Dioxygenase from Vibrio cholerae O1 biovar El Tor
Authors: Kim, Y. / Gu, M. / Hasseman, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionApr 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flavohemoprotein
B: Flavohemoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,38416
Polymers53,9832
Non-polymers2,40114
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Flavohemoprotein
hetero molecules

B: Flavohemoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,38416
Polymers53,9832
Non-polymers2,40114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-x+y,-z+1/31
Buried area6240 Å2
ΔGint-83 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.329, 93.329, 112.594
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Flavohemoprotein / Flavohemoglobin / Hemoglobin-like protein / Nitric oxide dioxygenase / NO oxygenase / NOD


Mass: 26991.371 Da / Num. of mol.: 2 / Fragment: FAD_NAD(P)H binding domain, UNP residues 152-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: hmp, VC_A0183 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q9KMY3, nitric oxide dioxygenase

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Non-polymers , 5 types, 226 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BisTris ph 6.5, 2.0 M ammonium sulphate, chymotrypsin (1:200), VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 28, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 29636 / Num. obs: 29636 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 34.5 Å2 / Rsym value: 0.12 / Net I/σ(I): 7.8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 1458 / Rsym value: 0.786 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_921)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→40.413 Å / SU ML: 0.3 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.01 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1483 5.07 %random
Rwork0.165 ---
all0.168 29265 --
obs0.168 29265 99.85 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.82 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso mean: 41.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.326 Å2-0 Å2-0 Å2
2--3.326 Å20 Å2
3----6.6521 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3721 0 151 212 4084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154169
X-RAY DIFFRACTIONf_angle_d1.4655693
X-RAY DIFFRACTIONf_dihedral_angle_d17.8071518
X-RAY DIFFRACTIONf_chiral_restr0.09604
X-RAY DIFFRACTIONf_plane_restr0.012734
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2002-2.27120.30621240.218425042628100
2.2712-2.35240.24081480.200824692617100
2.3524-2.44660.2451260.190825162642100
2.4466-2.55790.25621450.182924892634100
2.5579-2.69270.27671270.188124922619100
2.6927-2.86140.24871310.177624992630100
2.8614-3.08220.20711390.160925162655100
3.0822-3.39230.20161340.150325262660100
3.3923-3.88280.23471330.137225472680100
3.8828-4.89060.16031480.135525542702100
4.8906-40.41940.22711280.18892670279899
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)
12.9481-0.6390.83543.4008-1.77241.9422-0.0995-0.2738-0.1550.5926-0.0940.25860.53120.00920.15310.48050.01230.14970.29410.00020.343827.12213.206933.8392
24.1437-0.47030.9022.1482-0.14444.0793-0.1152-0.3676-0.39150.69810.14560.4344-0.134-0.0642-0.0520.33250.01150.06460.1528-0.00230.275633.480615.810734.8431
32.1433-0.37620.59289.68570.58956.8595-0.12340.2591-0.1098-0.519-0.22071.50480.9182-0.3350.19460.4330.03360.02110.2221-0.0490.466631.04896.164923.4659
42.5710.04084.20234.49341.07778.5987-0.23750.07480.06140.0318-0.04880.2459-0.16180.24790.20260.1989-0.00260.04540.18070.03550.261333.382617.596726.9052
53.8413-1.9498-0.47082.41941.16720.6042-0.260.0198-0.3917-0.12850.08460.24830.3827-0.26570.11410.3586-0.08740.02650.19560.0020.289425.599512.301625.5863
62.21110.3618-0.28972.2559-0.81351.75590.0042-0.16950.0050.12260.0679-0.04820.24290.0829-0.05230.22610.0071-0.00550.1988-0.00950.165945.193225.544533.7945
73.77150.0251.65442.9449-0.93148.0333-0.25060.34480.6247-0.13510.2055-0.0049-1.17110.06950.07410.3188-0.05110.00160.24890.04340.310245.622736.475723.6125
84.57311.09711.34534.46770.46365.4609-0.1802-0.01760.2982-0.11770.1165-0.1656-0.00950.39440.00230.23780.01220.03520.2772-0.05850.259456.379827.943927.1905
94.69971.3364-0.01466.065-0.68148.3127-0.08180.457-0.3375-0.17960.2038-0.19270.62840.1438-0.1250.2780.03470.01590.2773-0.05750.211356.127820.21223.6285
103.76212.27910.54852.20844.49734.98510.0203-0.1408-0.0132-0.0422-0.1187-0.17050.32060.05620.0770.2193-0.0031-0.01840.1870.06480.242422.458934.274329.6862
114.3656-0.2873-2.89863.4852-1.55886.64330.2321-0.09210.3105-0.0027-0.0247-0.2704-0.16250.2636-0.1950.16060.0315-0.02320.1814-0.02270.226816.995941.51427.7455
125.6304-0.9081-1.28696.6597-0.21797.74590.03921.2055-0.4045-1.15930.1602-0.51370.6951-0.6175-0.29190.3725-0.10110.04910.4384-0.08120.344617.59931.067918.1658
132.9534-1.7367-0.74861.2620.3992.16310.0844-0.01840.2727-0.06040.0911-0.30860.02050.1499-0.13840.2045-0.02440.00430.23290.03140.280824.804737.262121.9815
141.99760.1371-0.66974.08920.54392.6843-0.09630.177-0.37560.246-0.01890.05990.3743-0.47830.09630.2313-0.07910.00620.2639-0.02310.24514.766127.149333.3431
150.8772-0.6424-1.60821.07531.82334.198-0.410.3966-1.25060.0120.06980.65231.0383-1.42280.29970.5633-0.54410.17660.7428-0.28350.7167-0.557115.754227.1605
165.38031.58510.89841.75970.00751.1302-0.44951.0081-0.0236-0.24110.14060.21180.3665-1.59740.23350.3723-0.2438-0.0281.0129-0.11250.3651-5.878328.767322.3643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:14)
2X-RAY DIFFRACTION2chain 'A' and (resseq 15:39)
3X-RAY DIFFRACTION3chain 'A' and (resseq 40:59)
4X-RAY DIFFRACTION4chain 'A' and (resseq 60:84)
5X-RAY DIFFRACTION5chain 'A' and (resseq 85:103)
6X-RAY DIFFRACTION6chain 'A' and (resseq 104:170)
7X-RAY DIFFRACTION7chain 'A' and (resseq 171:188)
8X-RAY DIFFRACTION8chain 'A' and (resseq 189:210)
9X-RAY DIFFRACTION9chain 'A' and (resseq 211:238)
10X-RAY DIFFRACTION10chain 'B' and (resseq 3:26)
11X-RAY DIFFRACTION11chain 'B' and (resseq 27:68)
12X-RAY DIFFRACTION12chain 'B' and (resseq 69:84)
13X-RAY DIFFRACTION13chain 'B' and (resseq 85:103)
14X-RAY DIFFRACTION14chain 'B' and (resseq 104:170)
15X-RAY DIFFRACTION15chain 'B' and (resseq 171:203)
16X-RAY DIFFRACTION16chain 'B' and (resseq 204:239)

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