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- PDB-3hrd: Crystal structure of nicotinate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 3hrd
TitleCrystal structure of nicotinate dehydrogenase
Components(Nicotinate dehydrogenase ...) x 4
KeywordsOXIDOREDUCTASE / Selenium ligand / 2Fe-2S / Iron / Iron-sulfur / Metal-binding
Function / homology
Function and homology information


nicotinate dehydrogenase / nicotinate dehydrogenase activity / nicotinate catabolic process / FAD binding / 2 iron, 2 sulfur cluster binding / electron transfer activity / nucleotide binding / metal ion binding
Similarity search - Function
CO dehydrogenase flavoprotein, C-terminal domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / [2Fe-2S]-binding domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD binding domain in molybdopterin dehydrogenase / CO dehydrogenase flavoprotein C-terminal domain ...CO dehydrogenase flavoprotein, C-terminal domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / [2Fe-2S]-binding domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD binding domain in molybdopterin dehydrogenase / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding / Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily / [2Fe-2S]-binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily / [2Fe-2S] binding domain / Molybdopterin cofactor-binding domain / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / Beta-grasp domain / FAD-binding, type PCMH, subdomain 2 / 2Fe-2S iron-sulfur cluster binding domain / FAD-binding, type PCMH-like superfamily / Enolase-like; domain 1 / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / DNA polymerase; domain 1 / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PTERIN CYTOSINE DINUCLEOTIDE / DIOXOTHIOMOLYBDENUM(VI) ION / NICOTINIC ACID / NITRATE ION / SELENIUM ATOM / Nicotinate dehydrogenase medium molybdopterin subunit / Nicotinate dehydrogenase large molybdopterin subunit / Nicotinate dehydrogenase small FeS subunit / Nicotinate dehydrogenase FAD-subunit
Similarity search - Component
Biological speciesEubacterium barkeri (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWagener, N. / Pierik, A.J. / Hille, R. / Dobbek, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: The Mo-Se active site of nicotinate dehydrogenase
Authors: Wagener, N. / Pierik, A.J. / Ibdah, A. / Hille, R. / Dobbek, H.
History
DepositionJun 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Nicotinate dehydrogenase large molybdopterin subunit
B: Nicotinate dehydrogenase medium molybdopterin subunit
C: Nicotinate dehydrogenase FAD-subunit
D: Nicotinate dehydrogenase small FeS subunit
E: Nicotinate dehydrogenase large molybdopterin subunit
F: Nicotinate dehydrogenase medium molybdopterin subunit
G: Nicotinate dehydrogenase FAD-subunit
H: Nicotinate dehydrogenase small FeS subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,09228
Polymers261,4248
Non-polymers4,66820
Water17,186954
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46660 Å2
ΔGint-352 kcal/mol
Surface area75640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.069, 71.700, 214.485
Angle α, β, γ (deg.)90.000, 90.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Nicotinate dehydrogenase ... , 4 types, 8 molecules AEBFCGDH

#1: Protein Nicotinate dehydrogenase large molybdopterin subunit


Mass: 46549.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Eubacterium barkeri (bacteria) / References: UniProt: Q0QLF2
#2: Protein Nicotinate dehydrogenase medium molybdopterin subunit


Mass: 34506.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Eubacterium barkeri (bacteria) / References: UniProt: Q0QLF1
#3: Protein Nicotinate dehydrogenase FAD-subunit


Mass: 32663.508 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Eubacterium barkeri (bacteria) / References: UniProt: Q0QLF4
#4: Protein Nicotinate dehydrogenase small FeS subunit


Mass: 16993.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Eubacterium barkeri (bacteria) / References: UniProt: Q0QLF3

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Non-polymers , 10 types, 974 molecules

#5: Chemical ChemComp-SE / SELENIUM ATOM


Mass: 78.960 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Se
#6: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-MOS / DIOXOTHIOMOLYBDENUM(VI) ION


Mass: 161.012 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HMoO2S
#9: Chemical ChemComp-MCN / PTERIN CYTOSINE DINUCLEOTIDE


Mass: 696.501 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H22N8O13P2S2
#10: Chemical ChemComp-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO2
#11: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#12: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#13: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 954 / 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: 2.86 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG3350, Tris-HCl, NaNO3, glycerol, pH7.5, vapor diffusion, hanging drop, temperature 296K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 26, 2007 / Details: Osmic mirrors
RadiationMonochromator: Osmic Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 150056 / Num. obs: 148377 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 10.73
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.28 / Num. unique all: 18035 / % possible all: 96.9

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RM6

1rm6


Resolution: 2.2→29.43 Å / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: Isotropic / Cross valid method: Random / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.251 7408 4.9 %
Rwork0.213 --
all0.224 148377 -
obs0.224 148159 98.6 %
Solvent computationBsol: 34.825 Å2
Displacement parametersBiso max: 131.92 Å2 / Biso mean: 35.689 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-3.388 Å20 Å2-1.91 Å2
2--1.148 Å20 Å2
3----4.536 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18079 0 251 954 19284
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2111.5
X-RAY DIFFRACTIONc_scbond_it1.762
X-RAY DIFFRACTIONc_mcangle_it1.9752
X-RAY DIFFRACTIONc_scangle_it2.5112.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2MoSe.param
X-RAY DIFFRACTION3fes.param
X-RAY DIFFRACTION4fad_oc.param
X-RAY DIFFRACTION5water_rep.param

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