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- PDB-3nix: Crystal structure of flavoprotein/dehydrogenase from Cytophaga hu... -

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Basic information

Entry
Database: PDB / ID: 3nix
TitleCrystal structure of flavoprotein/dehydrogenase from Cytophaga hutchinsonii. Northeast Structural Genomics Consortium Target ChR43.
ComponentsFlavoprotein/dehydrogenase
KeywordsOXIDOREDUCTASE / Flavoprotein / dehydrogenase / Structural Genomics / PSI-2 / NESG / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Flavoprotein/dehydrogenase / Flavoprotein/dehydrogenase
Similarity search - Component
Biological speciesCytophaga hutchinsonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, SAD / Resolution: 2.6 Å
AuthorsVorobiev, S. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Maglaqui, M. / Everett, J.K. / Nair, R. ...Vorobiev, S. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Maglaqui, M. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of flavoprotein/dehydrogenase from Cytophaga hutchinsonii.
Authors: Vorobiev, S. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Maglaqui, M. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 6, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flavoprotein/dehydrogenase
B: Flavoprotein/dehydrogenase
C: Flavoprotein/dehydrogenase
D: Flavoprotein/dehydrogenase
E: Flavoprotein/dehydrogenase
F: Flavoprotein/dehydrogenase
G: Flavoprotein/dehydrogenase
H: Flavoprotein/dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)389,76016
Polymers383,4768
Non-polymers6,2848
Water16,448913
1
A: Flavoprotein/dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7202
Polymers47,9341
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Flavoprotein/dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7202
Polymers47,9341
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Flavoprotein/dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7202
Polymers47,9341
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Flavoprotein/dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7202
Polymers47,9341
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Flavoprotein/dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7202
Polymers47,9341
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Flavoprotein/dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7202
Polymers47,9341
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Flavoprotein/dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7202
Polymers47,9341
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Flavoprotein/dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7202
Polymers47,9341
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.224, 244.046, 100.222
Angle α, β, γ (deg.)90.000, 104.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Flavoprotein/dehydrogenase


Mass: 47934.473 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytophaga hutchinsonii (bacteria) / Strain: ATCC 33406/NCIMB 9469 / Gene: CHU_2822, fixC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q11R94, UniProt: A0A6N4SUC0*PLUS
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 913 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 13% PEG 2000, 0.01M magnesium chloride, 0.005M FAD, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 245330 / Num. obs: 238952 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 21.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 6.3 / Num. unique all: 24588 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.6_289refinement
PDB_EXTRACT3data extraction
Web-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
PHENIXphasing
REFMACrefinement
RefinementMethod to determine structure: molecular replacement, SAD
Starting model: 3I3L

3i3l


Resolution: 2.6→29.331 Å / Cross valid method: THROUGHOUT / σ(F): 0.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.264 11867 5.03 %RANDOM
Rwork0.237 ---
obs0.238 235949 96.85 %-
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.848 Å2
Baniso -1Baniso -2Baniso -3
1-5.8782 Å20 Å21.9981 Å2
2---2.8767 Å2-0 Å2
3----3.0016 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25515 0 424 913 26852
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_deg1.251
X-RAY DIFFRACTIONf_dihedral_angle_d20.377
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)
10.0144-0.0318-0.07290.25860.05150.2747-0.06150.0149-0.00090.0052-0.00830.04290.0130.01070.0423-0.0003-0.0008-0.01190.04990.01040.040155.7817115.47627.8487
20.07230.1357-0.02680.6273-0.06190.52070.01070.015-0.01320.0755-0.1061-0.0248-0.060.00640.06970.059-0.0364-0.02160.05490.02420.033544.2392117.587255.1977
30.05970.1005-0.00110.5995-0.02570.38340.0830.01420.0010.0753-0.1059-0.0051-0.03720.02110.01960.0588-0.065-0.00130.05610.00780.0386.8842121.267555.1727
40.02940.11-0.05780.60390.10940.26720.03850.01050.03560.01950.00390.00730.0089-0.0147-0.02170.047-0.0170.00090.08870.02670.110132.3477174.24321.6866
50.0086-0.050.04040.24020.00610.2371-0.05550.00460.0087-0.0161-0.0153-0.07680.0172-0.09750.04730.0802-0.04130.01790.112-0.01590.135662.7846179.847151.1539
60.009-0.0083-0.04870.2109-0.03440.2653-0.0195-0.00330.00570.02210.0030.02310.01790.01040.01320.0528-0.04410.00410.05890.00680.052998.4902119.26927.7963
70.0555-0.1464-0.07940.37830.06960.65050.01380.01610.0332-0.01830.0536-0.05050.034-0.0976-0.0520.0755-0.0526-0.01630.08040.04020.0921106.0898176.052451.3497
80.08370.1055-0.07540.50130.05820.1715-0.02010.0285-0.00490.0388-0.03120.04090.0131-0.04960.04050.0677-0.03340.00610.0815-0.02150.099175.4271177.7511.3401
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA4 - 414
2X-RAY DIFFRACTION2chain BB7 - 411
3X-RAY DIFFRACTION3chain CC4 - 412
4X-RAY DIFFRACTION4chain DD5 - 412
5X-RAY DIFFRACTION5chain FF6 - 412
6X-RAY DIFFRACTION6chain EE3 - 413
7X-RAY DIFFRACTION7chain GG3 - 413
8X-RAY DIFFRACTION8chain HH5 - 412

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