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- PDB-2bih: crystal structure of the Molybdenum-containing nitrate reducing f... -

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Basic information

Entry
Database: PDB / ID: 2bih
Titlecrystal structure of the Molybdenum-containing nitrate reducing fragment of Pichia angusta assimilatory nitrate reductase
ComponentsNITRATE REDUCTASE [NADPH]
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / NITRATE ASSIMILATION
Function / homology
Function and homology information


nitrate reductase (NADPH) / nitrate reductase (NADPH) activity / molybdenum ion binding / molybdopterin cofactor binding / nitrate assimilation / nitric oxide biosynthetic process / FAD binding / heme binding
Similarity search - Function
Nitrate reductase NADH dependent / Immunoglobulin-like - #650 / Sulfite Oxidase; Chain A, domain 2 / Oxidoreductase, molybdopterin-binding domain / Moybdenum cofactor oxidoreductase, dimerisation / Eukaryotic molybdopterin oxidoreductase / Mo-co oxidoreductase dimerisation domain / Oxidoreductase, molybdopterin-binding domain / Oxidoreductase molybdopterin binding domain / Oxidoreductase, molybdopterin-binding domain superfamily ...Nitrate reductase NADH dependent / Immunoglobulin-like - #650 / Sulfite Oxidase; Chain A, domain 2 / Oxidoreductase, molybdopterin-binding domain / Moybdenum cofactor oxidoreductase, dimerisation / Eukaryotic molybdopterin oxidoreductase / Mo-co oxidoreductase dimerisation domain / Oxidoreductase, molybdopterin-binding domain / Oxidoreductase molybdopterin binding domain / Oxidoreductase, molybdopterin-binding domain superfamily / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / 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 / Immunoglobulin E-set / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
(MOLYBDOPTERIN-S,S)-DIOXO-THIO-MOLYBDENUM(IV) / Nitrate reductase [NADPH]
Similarity search - Component
Biological speciesPICHIA ANGUSTA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFischer, K. / Barbier, G. / Hecht, H.-J. / Mendel, R.R. / Campbell, W.H. / Schwarz, G.
CitationJournal: Plant Cell / Year: 2005
Title: Structural Basis of Eukaryotic Nitrate Reduction: Crystal Structures of the Nitrate Reductase Active Site
Authors: Fischer, K. / Barbier, G. / Hecht, H.-J. / Mendel, R.R. / Campbell, W.H. / Schwarz, G.
History
DepositionJan 21, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NITRATE REDUCTASE [NADPH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9062
Polymers54,3881
Non-polymers5181
Water1,06359
1
A: NITRATE REDUCTASE [NADPH]
hetero molecules

A: NITRATE REDUCTASE [NADPH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,8124
Polymers108,7762
Non-polymers1,0372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area5890 Å2
ΔGint-27.3 kcal/mol
Surface area32060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.740, 76.740, 306.086
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein NITRATE REDUCTASE [NADPH] / ASSIMILATORY NITRATE REDUCTASE


Mass: 54387.883 Da / Num. of mol.: 1
Fragment: MOCO-BINDING DOMAIN, DIMERIZATION DOMAIN, RESIDUES 11-13,20-478
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PICHIA ANGUSTA (fungus) / Plasmid: SNAR1-PPICZB / Production host: PICHIA PASTORIS (fungus) / Strain (production host): Y-11430 / References: UniProt: P49050, EC: 1.7.1.2
#2: Chemical ChemComp-MTV / (MOLYBDOPTERIN-S,S)-DIOXO-THIO-MOLYBDENUM(IV)


Mass: 518.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9MoN5O8PS2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHIS TAG INSERTION OF (HHHHHHD) BETWEEN E13 AND I14
Nonpolymer detailsTHE HETGROUP CALLED MTV IN THIS PDB ENTRY IS SIMILAR TO MTQ EXCEPT FOR THE FACT THAT THE OM2-MO ...THE HETGROUP CALLED MTV IN THIS PDB ENTRY IS SIMILAR TO MTQ EXCEPT FOR THE FACT THAT THE OM2-MO BOND IS A REDUCED SINGLE BOND HAVING ONE EXTRA HYDROGEN. FOR METAL ATOM MOM1 MTV A1479 THE COORDINATION ANGLES ARE: 1 MTV 1479A S1' 2 MTV 1479A S2' 79.7 3 MTV 1479A OM2 82.6 142.1 4 MTV 1479A OM1 113.8 107.3 110.5 1 2 3
Sequence detailsTHE AUTHORS INDICATE THAT THE CONFLICT DESCRIBED BELOW IS PROBABLY DUE TO ERROR IN THE SEQUENCE ...THE AUTHORS INDICATE THAT THE CONFLICT DESCRIBED BELOW IS PROBABLY DUE TO ERROR IN THE SEQUENCE DATABASE ANNOTATION, SINCE IN THIS STRUCTURE AS WELL IN THE HIGH RESOLUTION STRUCTURE (PDB ID: 2BII), NO SIDE CHAIN DENSITY FOR AN ARGININE COULD BE OBSERVED. N-TERMINAL SEQUENCING OF THE PROTEIN CRYSTAL CONFIRMS THAT THE SEQUENCE BEINGS AT RESIDUE 11. RESIDUES RESIDUES 479-484 ARE NOT VISIBLE IN THE CRYSTAL STRUCTURE

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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: 2.3 Å3/Da / Density % sol: 47 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.005
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 26, 2003 / Details: MIRRORS
RadiationMonochromator: SI DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 17438 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 24.7
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OGP

1ogp


Resolution: 2.6→65.94 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.901 / SU B: 21.854 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / ESU R: 0.785 / ESU R Free: 0.325 / Stereochemistry target values: RESTRAINED TLS / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 880 5.17 %RANDOM
Rwork0.19 ---
obs0.193 17366 99.6 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 46.81 Å2
Baniso -1Baniso -2Baniso -3
1-2.454 Å21.227 Å20 Å2
2--2.454 Å20 Å2
3----3.681 Å2
Refinement stepCycle: LAST / Resolution: 2.6→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3654 0 27 59 3740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223784
X-RAY DIFFRACTIONr_bond_other_d0.0020.023366
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.9575140
X-RAY DIFFRACTIONr_angle_other_deg0.84837829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4065452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90823.371178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60115637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8661531
X-RAY DIFFRACTIONr_chiral_restr0.090.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024193
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02793
X-RAY DIFFRACTIONr_nbd_refined0.2170.2817
X-RAY DIFFRACTIONr_nbd_other0.2030.23664
X-RAY DIFFRACTIONr_nbtor_refined0.1910.21846
X-RAY DIFFRACTIONr_nbtor_other0.0920.22209
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2141
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5350.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8731.52840
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04223654
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6531871
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4744.51486
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 11.46→65.94 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.444 9
Rwork0.246 239
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)
10.48-0.0502-0.09640.38760.09450.67760.03510.0435-0.0952-0.0953-0.03370.02370.15220.0917-0.00140.040.0641-0.0394-0.0431-0.0308-0.05353.0522-2.629111.0992
20.6562-0.16640.02360.38130.06930.53250.031-0.0794-0.0397-0.0686-0.03320.09510.0837-0.06640.0022-0.02980.0056-0.0313-0.0386-0.0247-0.022337.54788.6078125.1463
33.49922.1102-9.52681.2726-5.745225.9371-0.2801-0.04180.0810.04520.17330.01590.7560.17730.10670.00680.0532-0.061-0.0106-0.0597-0.015950.08420.3261108.5658
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 274
2X-RAY DIFFRACTION2A275 - 478
3X-RAY DIFFRACTION3A1479

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