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- PDB-2nap: DISSIMILATORY NITRATE REDUCTASE (NAP) FROM DESULFOVIBRIO DESULFURICANS -

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Basic information

Entry
Database: PDB / ID: 2nap
TitleDISSIMILATORY NITRATE REDUCTASE (NAP) FROM DESULFOVIBRIO DESULFURICANS
ComponentsPROTEIN (PERIPLASMIC NITRATE REDUCTASE)
KeywordsOXIDOREDUCTASE / NITROGENOUS ACCEPTOR / DISSIMILATORY NITRATE REDUCTASE / MULTIWAVELENGTH ANOMALOUS DIFFRACTION / MOLYBDOPTERIN COFACTOR / [4FE-4S] CLUSTER
Function / homology
Function and homology information


nitrate reductase (cytochrome) / nitrate reductase (cytochrome) activity / nitrate reductase complex / molybdenum ion binding / Mo-molybdopterin cofactor biosynthetic process / molybdopterin cofactor binding / cellular respiration / nitrate assimilation / 4 iron, 4 sulfur cluster binding / electron transfer activity ...nitrate reductase (cytochrome) / nitrate reductase (cytochrome) activity / nitrate reductase complex / molybdenum ion binding / Mo-molybdopterin cofactor biosynthetic process / molybdopterin cofactor binding / cellular respiration / nitrate assimilation / 4 iron, 4 sulfur cluster binding / electron transfer activity / periplasmic space / iron ion binding / membrane
Similarity search - Function
Periplasmic nitrate reductase, large subunit / Nitrate reductase NapA-like, molybdopterin-binding domain / ADC-like domains / Rossmann fold - #740 / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain ...Periplasmic nitrate reductase, large subunit / Nitrate reductase NapA-like, molybdopterin-binding domain / ADC-like domains / Rossmann fold - #740 / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / N-terminal domain of TfIIb / : / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Single Sheet / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-MGD / MOLYBDENUM ATOM / IRON/SULFUR CLUSTER / : / Periplasmic nitrate reductase
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsDias, J.M. / Than, M. / Humm, A. / Huber, R. / Bourenkov, G. / Bartunik, H. / Bursakov, S. / Calvete, J. / Caldeira, J. / Carneiro, C. ...Dias, J.M. / Than, M. / Humm, A. / Huber, R. / Bourenkov, G. / Bartunik, H. / Bursakov, S. / Calvete, J. / Caldeira, J. / Carneiro, C. / Moura, J. / Moura, I. / Romao, M.J.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structure of the first dissimilatory nitrate reductase at 1.9 A solved by MAD methods.
Authors: Dias, J.M. / Than, M.E. / Humm, A. / Huber, R. / Bourenkov, G.P. / Bartunik, H.D. / Bursakov, S. / Calvete, J. / Caldeira, J. / Carneiro, C. / Moura, J.J. / Moura, I. / Romao, M.J.
History
DepositionSep 18, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 6, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_distant_solvent_atoms ...atom_site / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_struct_conn_angle.value
Revision 2.1Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_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_label_atom_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_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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Aug 12, 2026Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id ..._pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_label_atom_id
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PERIPLASMIC NITRATE REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5176
Polymers80,3931
Non-polymers2,1245
Water10,719595
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.260, 106.260, 134.910
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, 1 molecules A

#1: Protein PROTEIN (PERIPLASMIC NITRATE REDUCTASE)


Mass: 80392.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio desulfuricans (bacteria) / Cellular location: PERIPLASM / References: GenBank: CAA77019, UniProt: P81186*PLUS

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Non-polymers , 5 types, 600 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mo
#4: Chemical ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.73 Å3/Da / Density % sol: 59 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
Common name: PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.7219,1.7389,1.1000
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1997
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.72191
21.73891
31.11
ReflectionResolution: 1.9→25 Å / Num. obs: 69767 / % possible obs: 98 % / Redundancy: 3.4 % / Rsym value: 0.053 / Net I/σ(I): 25.9
Reflection shellResolution: 1.9→1.93 Å / Mean I/σ(I) obs: 4 / Rsym value: 0.436 / % possible all: 93.5
Reflection
*PLUS
Num. measured all: 1048219 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 93.5 % / Rmerge(I) obs: 0.436

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Processing

Software
NameVersionClassification
CCP4model building
SHARPphasing
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.267 4225 5 %RANDOM
Rwork0.218 ---
obs0.218 66798 96.1 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5591 0 115 595 6301
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.01
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.01

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