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- PDB-2e81: Cytochrome c Nitrite Reductase from Wolinella succinogenes with b... -

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Basic information

Entry
Database: PDB / ID: 2.0E+81
TitleCytochrome c Nitrite Reductase from Wolinella succinogenes with bound intermediate hydroxylamine
ComponentsCytochrome c-552
KeywordsOXIDOREDUCTASE / multiheme cytochrome / nitrite reductase / reaction intermediate
Function / homology
Function and homology information


nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / anaerobic electron transport chain / anaerobic respiration / nitrate assimilation / outer membrane-bounded periplasmic space / 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
PROTOPORPHYRIN IX CONTAINING FE / HYDROXYAMINE / YTTRIUM (III) ION / Cytochrome c-552
Similarity search - Component
Biological speciesWolinella succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEinsle, O. / Kroneck, P.M.H.
Citation
Journal: J.Am.Chem.Soc. / Year: 2002
Title: Mechanism of the six-electron reduction of nitrite to ammonia by cytochrome c nitrite reductase
Authors: Einsle, O. / Messerschmidt, A. / Huber, R. / Kroneck, P.M.H. / Neese, F.
#1: Journal: Nature / Year: 1999
Title: Structure of cytochrome c nitrite reductase
Authors: Einsle, O. / Messerschmidt, A. / Stach, P. / Bourenkov, G.P. / Bartunik, H.D. / Huber, R. / Kroneck, P.M.H.
#2: Journal: J.Biol.Chem. / Year: 2000
Title: Cytochrome c nitrite reductase from Wolinella succinogenes. Structure at 1.6 A resolution, inhibitor binding, and heme-packing motifs
Authors: Einsle, O. / Stach, P. / Messerschmidt, A. / Simon, J. / Kroeger, A. / Huber, R. / Kroneck, P.M.H.
History
DepositionJan 15, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 25, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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

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Assembly

Deposited unit
A: Cytochrome c-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,76611
Polymers55,3441
Non-polymers3,42210
Water7,764431
1
A: Cytochrome c-552
hetero molecules

A: Cytochrome c-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,53222
Polymers110,6872
Non-polymers6,84520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_565-x,-y+1,z1
Buried area16900 Å2
ΔGint-322 kcal/mol
Surface area36700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)119.891, 119.891, 186.224
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-803-

YT3

DetailsBiological unit is a dimer, created by the crystallographic twofold axis.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome c-552 / Ammonia-forming cytochrome c nitrite reductase / Cytochrome c nitrite reductase


Mass: 55343.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Wolinella succinogenes (bacteria) / Strain: DSM 1740
References: UniProt: Q9S1E5, nitrite reductase (cytochrome; ammonia-forming)

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Non-polymers , 5 types, 441 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Y
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-HOA / HYDROXYAMINE


Mass: 33.030 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H3NO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 12% PEG 4000, 0.2M ammonium sulfate, 0.015M yttrium chloride, 0.1M sodium acetate, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 10, 2001 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 46010 / Num. obs: 45781 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.8
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MAR345data collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FS7

1fs7


Resolution: 2→25 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 2292 -random
Rwork0.1865 ---
all-45751 --
obs-43459 99.4 %-
Displacement parametersBiso mean: 38.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.21 Å20 Å20 Å2
2---3.21 Å20 Å2
3---6.421 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3772 0 221 431 4424
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006074
X-RAY DIFFRACTIONc_angle_deg2.25908

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