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- PDB-3ml1: Crystal Structure of the Periplasmic Nitrate Reductase from Cupri... -

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Basic information

Entry
Database: PDB / ID: 3ml1
TitleCrystal Structure of the Periplasmic Nitrate Reductase from Cupriavidus necator
Components
  • Diheme cytochrome c napB
  • Periplasmic nitrate reductase
KeywordsOXIDOREDUCTASE / Heterodimer
Function / homology
Function and homology information


nitrate reductase (cytochrome) / nitrate reductase (cytochrome) activity / nitrate reductase activity / oxidoreductase complex / Mo-molybdopterin cofactor biosynthetic process / molybdenum ion binding / molybdopterin cofactor binding / cellular respiration / anaerobic respiration / nitrate assimilation ...nitrate reductase (cytochrome) / nitrate reductase (cytochrome) activity / nitrate reductase activity / oxidoreductase complex / Mo-molybdopterin cofactor biosynthetic process / molybdenum ion binding / molybdopterin cofactor binding / cellular respiration / anaerobic respiration / nitrate assimilation / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / iron ion binding / metal ion binding
Similarity search - Function
Phosphorylase Kinase; domain 1 - #210 / Nitrate reductase cytochrome c-type subunit NapB / Nitrate reductase cytochrome c-type subunit (NapB) / Periplasmic nitrate reductase, large subunit / Nitrate reductase NapA-like, molybdopterin-binding domain / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Rossmann fold - #740 / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. ...Phosphorylase Kinase; domain 1 - #210 / Nitrate reductase cytochrome c-type subunit NapB / Nitrate reductase cytochrome c-type subunit (NapB) / Periplasmic nitrate reductase, large subunit / Nitrate reductase NapA-like, molybdopterin-binding domain / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Rossmann fold - #740 / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Molybdopterin oxidoreductase Fe4S4 domain / Multiheme cytochrome c family profile. / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Multiheme cytochrome superfamily / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Phosphorylase Kinase; domain 1 / Beta Barrel / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HEME C / Chem-MGD / DIOXOTHIOMOLYBDENUM(VI) ION / IRON/SULFUR CLUSTER / Periplasmic nitrate reductase / Periplasmic nitrate reductase, electron transfer subunit
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsCoelho, C. / Trincao, J. / Romao, M.J.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The crystal structure of Cupriavidus necator nitrate reductase in oxidized and partially reduced states
Authors: Coelho, C. / Gonzalez, P.J. / Moura, J.J.G. / Moura, I. / Trincao, J. / Romao, M.J.
History
DepositionApr 16, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 7, 2011Group: Database references
Revision 1.3Nov 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_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.pdbx_leaving_atom_flag / _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_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: Periplasmic nitrate reductase
B: Diheme cytochrome c napB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1368
Polymers105,9052
Non-polymers3,2316
Water12,106672
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-32 kcal/mol
Surface area31390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.202, 82.384, 96.837
Angle α, β, γ (deg.)90.00, 100.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Periplasmic nitrate reductase / NapA


Mass: 90512.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Catalytic subunit / Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: H16 / Gene: napAB / Plasmid: pCM62 / Production host: Cupriavidus necator (bacteria) / Strain (production host): HF210 / References: UniProt: P39185, nitrate reductase
#2: Protein Diheme cytochrome c napB / NapB


Mass: 15392.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: H16 / Gene: napB / Plasmid: pCM62 / Production host: Cupriavidus necator (bacteria) / Strain (production host): HF210 / References: UniProt: P39186, nitrate reductase (cytochrome)

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Non-polymers , 5 types, 678 molecules

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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-MOS / DIOXOTHIOMOLYBDENUM(VI) ION


Mass: 161.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HMoO2S
#5: 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
#6: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE RESIDUE A 900 WAS ORIGINALLY DEPOSITED AS A ISOLATED SULFUR ATOM. THE HETEROGEN S IS NOW ...THE RESIDUE A 900 WAS ORIGINALLY DEPOSITED AS A ISOLATED SULFUR ATOM. THE HETEROGEN S IS NOW OBSOLETE IN THE PDB HETGROUP DICTIONARY. IN THIS ENTRY, IT IS TREATED AS A PART OF MOS A1802. OTHER SULFURS OF MOLYBDENUM ATOM ARE SUPPLIED FROM SURROUNDING MGDS.

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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: 2.63 Å3/Da / Density % sol: 53.25 % / Mosaicity: 0.561 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M bis-Tris pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jul 15, 2006 / Details: Sagitally focusing Ge(220) and a multilayer
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.5→95.346 Å / Num. all: 170014 / Num. obs: 170014 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 8.5
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 1.3 / Num. measured all: 92176 / Num. unique all: 24265 / Rsym value: 0.537 / % possible all: 95.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å39.69 Å
Translation2.5 Å39.69 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 170003
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.13-10031.10.6181067
5.75-8.1336.60.732028
4.69-5.7534.60.7482611
4.07-4.6934.60.7783089
3.64-4.07370.7573474
3.32-3.6439.30.743842
3.07-3.3243.30.7244187
2.87-3.0745.70.7174476
2.71-2.8747.60.714735
2.57-2.7149.80.7094989
2.45-2.5752.90.695284
2.35-2.4553.70.7075465
2.26-2.3553.80.7065750
2.17-2.2656.50.75911
2.1-2.1756.40.7156121
2.03-2.160.60.686341
1.97-2.0361.20.6916522
1.92-1.9762.20.6926685
1.87-1.9262.80.7166875
1.82-1.8764.40.6977070
1.77-1.8265.10.7147249
1.73-1.7766.30.7247354
1.7-1.73670.7187528
1.66-1.768.30.727732
1.63-1.6669.80.7067826
1.59-1.6369.70.7287983
1.56-1.5969.40.7178095
1.54-1.5670.40.7158287
1.5-1.5473.90.61211427

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.19data scaling
PHASER1.3.1phasing
DM6phasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NAP

2nap


Resolution: 1.6→35.48 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 2.847 / SU ML: 0.051 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES; WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.19031 7066 5 %RANDOM
Rwork0.15707 133743 --
obs0.15875 140809 97.36 %-
all-254265 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.39 Å2 / Biso mean: 15.87 Å2 / Biso min: 5.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.01 Å2
2---0.08 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.6→35.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7208 0 190 672 8070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0227697
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2662.00510554
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8865926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52323.465355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.991151233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0111555
X-RAY DIFFRACTIONr_chiral_restr0.2070.21089
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0215958
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1371.54565
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77827371
X-RAY DIFFRACTIONr_scbond_it2.9533132
X-RAY DIFFRACTIONr_scangle_it4.3514.53110
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 494 -
Rwork0.254 9796 -
all-10290 -
obs--96.18 %
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)
10.776-0.1258-0.03680.78070.06950.98910.02370.01450.0840.0257-0.0398-0.0802-0.03650.14390.01610.0414-0.00260.00110.07480.0220.068858.537-4.71627.452
20.66010.00110.04590.6127-0.09270.80310.01550.19440.1076-0.1103-0.0453-0.0669-0.08730.09040.02980.10270.02560.01660.12410.04450.064649.934-0.3086.422
30.64-0.23530.03520.56330.02690.6540.007-0.03430.0453-0.0011-0.02430.049-0.0696-0.14010.01730.04660.01570.00380.0621-0.01760.063128.747-2.40235.592
40.5837-0.1544-0.0250.52880.08330.63620.03760.0372-0.039-0.0245-0.05250.03990.0575-0.09540.01490.05070.00360.00060.0557-0.00670.037832.791-15.19825.12
51.59650.38130.12851.75070.05211.22680.14170.071-0.2365-0.0117-0.0639-0.04590.24360.1217-0.07780.16630.0311-0.00970.1061-0.04870.1243.208-31.84515.678
61.923-0.1974-0.18832.05660.65993.18840.0588-0.2146-0.09470.0737-0.0375-0.05890.05860.0176-0.02120.0642-0.0086-0.00570.06910.01970.091950.125-25.06146.029
74.7122.6301-1.29652.10490.30272.08370.023-0.041-0.46210.15670.1004-0.40110.30520.3365-0.12340.22190.1391-0.0380.1942-0.02610.211459.531-29.58224.063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 68
2X-RAY DIFFRACTION1A502 - 530
3X-RAY DIFFRACTION1A600 - 640
4X-RAY DIFFRACTION2A69 - 147
5X-RAY DIFFRACTION2A387 - 501
6X-RAY DIFFRACTION2A531 - 599
7X-RAY DIFFRACTION3A148 - 386
8X-RAY DIFFRACTION4A641 - 802
9X-RAY DIFFRACTION5B1 - 27
10X-RAY DIFFRACTION6B37 - 65
11X-RAY DIFFRACTION6B72 - 104
12X-RAY DIFFRACTION7B105 - 122

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