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- PDB-3tor: Crystal structure of Escherichia coli NrfA with Europium bound -

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Basic information

Entry
Database: PDB / ID: 3tor
TitleCrystal structure of Escherichia coli NrfA with Europium bound
ComponentsCytochrome c nitrite reductase
KeywordsOXIDOREDUCTASE / Multihaem cytochrome / decaheme / reductase / Electron transport / Iron / Metal-binding / Nitrite / Calcium binding
Function / homology
Function and homology information


nitric oxide reductase activity / nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / anaerobic electron transport chain / nitrate assimilation / outer membrane-bounded periplasmic space / iron ion binding / heme binding / calcium ion binding
Similarity search - Function
Formate-dependent cytochrome c nitrite reductase, c552 subunit / Cytochrome c552 / Cytochrome c552 / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Multiheme cytochrome c family profile. / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Multiheme cytochrome superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle ...Formate-dependent cytochrome c nitrite reductase, c552 subunit / Cytochrome c552 / Cytochrome c552 / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Multiheme cytochrome c family profile. / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Multiheme cytochrome superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
EUROPIUM ION / HEME C / Cytochrome c-552
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLockwood, C.W.J. / Clarke, T.A. / Butt, J.N. / Hemmings, A.M. / Richardson, D.J.
CitationJournal: Biochem.Soc.Trans. / Year: 2011
Title: Characterization of the active site and calcium binding in cytochrome c nitrite reductases.
Authors: Lockwood, C.W. / Clarke, T.A. / Butt, J.N. / Hemmings, A.M. / Richardson, D.J.
History
DepositionSep 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_conn_type / 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_alt_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_alt_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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: Cytochrome c nitrite reductase
B: Cytochrome c nitrite reductase
C: Cytochrome c nitrite reductase
D: Cytochrome c nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,57137
Polymers202,6724
Non-polymers13,89833
Water36,9312050
1
A: Cytochrome c nitrite reductase
D: Cytochrome c nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,20918
Polymers101,3362
Non-polymers6,87316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16210 Å2
ΔGint-304 kcal/mol
Surface area33390 Å2
MethodPISA
2
B: Cytochrome c nitrite reductase
C: Cytochrome c nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,36119
Polymers101,3362
Non-polymers7,02517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16300 Å2
ΔGint-306 kcal/mol
Surface area33520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.884, 90.489, 292.196
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
Cytochrome c nitrite reductase / Ammonia-forming cytochrome c nitrite reductase / Cytochrome c-552


Mass: 50668.117 Da / Num. of mol.: 4 / Fragment: Cytochrome c nitrite reductase / Source method: isolated from a natural source / Details: Periplasm / Source: (natural) Escherichia coli (E. coli) / Strain: LCB 2048
References: UniProt: P0ABK9, nitrite reductase (cytochrome; ammonia-forming)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EU / EUROPIUM ION


Mass: 151.964 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Eu
#4: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2050 / 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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Crystals were obtained in 100 mM HEPES pH 7.5, 20 % PEG 10 K. Soaked in mother liqour containing 10 mM Eu(II)Cl, 20 % Ethylene glycol for 2 minutes before immersion in liquid nitrogen., ...Details: Crystals were obtained in 100 mM HEPES pH 7.5, 20 % PEG 10 K. Soaked in mother liqour containing 10 mM Eu(II)Cl, 20 % Ethylene glycol for 2 minutes before immersion in liquid nitrogen., VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 17, 2001
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→146.1 Å / Num. obs: 139682 / % possible obs: 98.5 % / Redundancy: 3.01 % / Biso Wilson estimate: 16.4 Å2 / Rsym value: 0.079 / Net I/σ(I): 11.6
Reflection shellResolution: 2→2.053 Å / Redundancy: 2.72 % / Mean I/σ(I) obs: 8.73 / Num. unique all: 9181 / Rsym value: 0.313 / % possible all: 93.28

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RDZ

2rdz


Resolution: 2→146.1 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.86 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22194 6985 5 %RANDOM
Rwork0.16355 ---
obs0.16646 132196 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.12 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å20 Å20 Å2
2---0.55 Å20 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 2→146.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13904 0 873 2050 16827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02215261
X-RAY DIFFRACTIONr_angle_refined_deg1.8542.11420932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41351760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50324.964699
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.058152475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4941572
X-RAY DIFFRACTIONr_chiral_restr0.1270.22016
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02111892
X-RAY DIFFRACTIONr_mcbond_it1.0821.58808
X-RAY DIFFRACTIONr_mcangle_it1.825214116
X-RAY DIFFRACTIONr_scbond_it3.23736453
X-RAY DIFFRACTIONr_scangle_it4.7594.56816
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 445 -
Rwork0.223 9181 -
obs--93.28 %

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