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- PDB-3bng: W. succinogenes NrfA Y218F -

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Basic information

Entry
Database: PDB / ID: 3bng
TitleW. succinogenes NrfA Y218F
ComponentsCytochrome c-552
KeywordsOXIDOREDUCTASE / c-type cytochrome / nitrite reductase / Calcium / Electron transport / Heme / Iron / Metal-binding / Periplasm / Transport
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 / calcium ion binding / heme 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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / YTTRIUM ION / Cytochrome c-552
Similarity search - Component
Biological speciesWolinella succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLukat, P. / Einsle, O.
CitationJournal: Biochemistry / Year: 2008
Title: Binding and Reduction of Sulfite by Cytochrome c Nitrite Reductase
Authors: Lukat, P. / Rudolf, M. / Stach, P. / Messerschmidt, A. / Kroneck, P.M.H. / Simon, J. / Einsle, O.
History
DepositionDec 14, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)59,17516
Polymers55,3281
Non-polymers3,84715
Water11,692649
1
A: Cytochrome c-552
hetero molecules

A: Cytochrome c-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,35032
Polymers110,6552
Non-polymers7,69530
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_565-x,-y+1,z1
Buried area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.030, 120.030, 186.276
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-512-

Y1

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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: 55327.605 Da / Num. of mol.: 1 / Mutation: Y218F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolinella succinogenes (bacteria) / Gene: nrfA Y218F / Production host: Wolinella succinogenes (bacteria)
References: UniProt: Q9S1E5, nitrite reductase (cytochrome; ammonia-forming)

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Non-polymers , 6 types, 664 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-Y1 / YTTRIUM ION


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


Mass: 616.487 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 649 / 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: 3.03 Å3/Da / Density % sol: 59.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: PEG 4000, ammonium sulfate, yttrium chloride, acetate buffer, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 5, 2007
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 109091 / Num. obs: 108437 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rsym value: 0.122 / Net I/σ(I): 14.4
Reflection shellResolution: 1.5→1.6 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.663 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.3.0008refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FS7

1fs7


Resolution: 1.5→42.45 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.291 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.077 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21506 5396 5 %RANDOM
Rwork0.18088 ---
obs0.18259 102080 98.71 %-
all-109091 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.5→42.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3807 0 242 649 4698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224152
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.482.1125676
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3565482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.524.946184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05715710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6871515
X-RAY DIFFRACTIONr_chiral_restr0.10.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023189
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2610.22403
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22795
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2577
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1550.212
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3060.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2040.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3021.52423
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.90323792
X-RAY DIFFRACTIONr_scbond_it3.5432017
X-RAY DIFFRACTIONr_scangle_it4.0314.51868
X-RAY DIFFRACTIONr_rigid_bond_restr3.41834440
X-RAY DIFFRACTIONr_sphericity_free5.4263654
X-RAY DIFFRACTIONr_sphericity_bonded3.80834025
LS refinement shellResolution: 1.496→1.535 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 351 -
Rwork0.348 6785 -
obs--89.39 %

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