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- PDB-1xhc: NADH oxidase /nitrite reductase from Pyrococcus furiosus Pfu-1140... -

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Basic information

Entry
Database: PDB / ID: 1xhc
TitleNADH oxidase /nitrite reductase from Pyrococcus furiosus Pfu-1140779-001
ComponentsNADH oxidase /nitrite reductase
KeywordsOXIDOREDUCTASE / NADH oxidase / nitrite reductase / Pyrococcus furiosus / Southeast Collaboratory for Structural Genomics / SECSG / hyperthermophile / protein structure initiative / PSI
Function / homology
Function and homology information


flavin adenine dinucleotide binding / oxidoreductase activity
Similarity search - Function
FAD/NAD-linked reductase, C-terminal dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADH oxidase /nitrite reductase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsHoranyi, P. / Tempel, W. / Weinberg, M.V. / Liu, Z.-J. / Shah, A. / Chen, L. / Lee, D. / Sugar, F.J. / Brereton, P.S. / Izumi, M. ...Horanyi, P. / Tempel, W. / Weinberg, M.V. / Liu, Z.-J. / Shah, A. / Chen, L. / Lee, D. / Sugar, F.J. / Brereton, P.S. / Izumi, M. / Poole II, F.L. / Shah, C. / Jenney Jr., F.E. / Arendall III, W.B. / Rose, J.P. / Adams, M.W.W. / Richardson, J.S. / Richardson, D.C. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: NADH oxidase /nitrite reductase from Pyrococcus furiosus Pfu-1140779-001
Authors: Horanyi, P. / Tempel, W. / Weinberg, M.V. / Liu, Z.-J. / Shah, A. / Chen, L. / Lee, D. / SUGAR, F.J. / BRERETON, P.S. / IZUMI, M. / POOLE II, F.L. / SHAH, C. / Jenney Jr., F.E. / Arendall ...Authors: Horanyi, P. / Tempel, W. / Weinberg, M.V. / Liu, Z.-J. / Shah, A. / Chen, L. / Lee, D. / SUGAR, F.J. / BRERETON, P.S. / IZUMI, M. / POOLE II, F.L. / SHAH, C. / Jenney Jr., F.E. / Arendall III, W.B. / Rose, J.P. / ADAMS, M.W.W. / Richardson, J.S. / Richardson, D.C. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics
History
DepositionSep 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 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
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADH oxidase /nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6932
Polymers40,9081
Non-polymers7861
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.335, 73.737, 95.849
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 NADH oxidase /nitrite reductase


Mass: 40907.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1K9
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.6152.79
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
3151modified microbatch3.814%w/v PEG-4000, 0.15M sodium chloride, 0.15M magnesium chloride, 0.1M sodium acetate, modified microbatch, temperature 315K, pH 3.8
3152modified microbatch3.818%w/v PEG-4000, 0.15M sodium chloride, 0.15M magnesium chloride, 0.1M sodium acetate, modified microbatch, temperature 315K, pH 3.8

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 17-ID11
SYNCHROTRONAPS 17-ID21
Detector
TypeIDDetector
ADSC QUANTUM 2101CCD
ADSC QUANTUM 2102CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 22114 / % possible obs: 92.2 % / Rmerge(I) obs: 0.112 / Χ2: 1.203
Reflection shell
Resolution (Å)Rmerge(I) obsNum. measured allΧ2Diffraction-ID% possible all
2.15-2.320.47430450.9391,264.5
2.32-2.550.42545200.9881,296
2.55-2.920.27547381.1651,2100
2.92-3.670.12648191.2711,2100
3.67-200.07649921.3231,2100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.2.0003refinement
PDB_EXTRACT1data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1F3P

1f3p


Resolution: 2.35→58.722 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.2 / SU B: 14.704 / SU ML: 0.168 / SU R Cruickshank DPI: 0.313 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.313 / ESU R Free: 0.229 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2412 915 5.025 %RANDOM
Rwork0.2 ---
all0.202 ---
obs0.20202 18210 99.378 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 37.008 Å2
Baniso -1Baniso -2Baniso -3
1-0.689 Å20 Å20 Å2
2--0.965 Å20 Å2
3----1.654 Å2
Refinement stepCycle: LAST / Resolution: 2.35→58.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 53 31 2721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222743
X-RAY DIFFRACTIONr_bond_other_d0.0020.022555
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.9843714
X-RAY DIFFRACTIONr_angle_other_deg0.79335903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5535344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.40224.196112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94615463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0271515
X-RAY DIFFRACTIONr_chiral_restr0.0840.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023031
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02544
X-RAY DIFFRACTIONr_nbd_refined0.1890.2422
X-RAY DIFFRACTIONr_nbd_other0.1690.22440
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21303
X-RAY DIFFRACTIONr_nbtor_other0.080.21642
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.264
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0310.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3080.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2050.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.25
X-RAY DIFFRACTIONr_mcbond_it0.771.51895
X-RAY DIFFRACTIONr_mcbond_other0.1271.5720
X-RAY DIFFRACTIONr_mcangle_it1.06222723
X-RAY DIFFRACTIONr_mcangle_other0.51122341
X-RAY DIFFRACTIONr_scbond_it1.55831229
X-RAY DIFFRACTIONr_scbond_other0.58932171
X-RAY DIFFRACTIONr_scangle_it2.4574.5991
X-RAY DIFFRACTIONr_scangle_other0.9214.53562
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.4110.341570.2471148126595.257
2.411-2.4770.293620.2371208128199.141
2.477-2.5490.289700.2311201127499.765
2.549-2.6270.303710.23911661237100
2.627-2.7130.31470.23511441191100
2.713-2.8080.274560.22910991155100
2.808-2.9140.256580.22610471105100
2.914-3.0320.274670.21310071074100
3.032-3.1670.283500.19810081058100
3.167-3.3210.26540.197937991100
3.321-3.50.238550.209891946100
3.5-3.7120.181350.182872907100
3.712-3.9670.212510.176801852100
3.967-4.2830.212430.166748791100
4.283-4.6890.203380.149694732100
4.689-5.2380.16280.163643671100
5.238-6.0410.268230.233588611100
6.041-7.3790.181230.222492515100
7.379-10.3540.292180.185397415100
10.354-58.7220.22290.26620425384.19
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)
10.27740.55590.5233.96162.7936.50590.17850.002-0.08330.48540.1853-0.3290.44440.2958-0.3638-0.11110.0592-0.0635-0.0710.0257-0.103741.619245.668532.8653
20.35670.0995-0.20761.41891.38673.29140.01070.037-0.03410.03390.011-0.0347-0.00660.0067-0.0217-0.15020.023-0.0133-0.08210.0378-0.077234.590352.978823.3202
313.0051-15.6305-10.498619.518414.597920.656-0.36590.2740.58420.45870.53410.3956-1.53620.4522-0.16820.2086-0.09180.12450.05510.03230.119651.434570.99978.8889
49.7396-2.9614-3.435624.471811.602913.69750.0473-0.748-0.24830.48730.1912-1.899-0.29831.0862-0.2385-0.0002-0.11060.05340.10520.12020.156254.829863.804415.2687
58.1985-3.1015-15.53691.54014.776132.7516-0.04421.0276-0.0052-0.02820.39540.08880.8764-0.6014-0.3512-0.17080.0243-0.0216-0.1313-0.0108-0.158236.326550.514827.2597
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A

IDRefine TLS-IDLabel asym-IDAuth seq-IDLabel seq-ID
11A1 - 569 - 64
22A57 - 31565 - 323
33A316 - 330324 - 338
44A336 - 351344 - 359
55B3601

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