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- PDB-3ubr: Laue structure of Shewanella oneidensis cytochrome-c Nitrite Reductase -

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Basic information

Entry
Database: PDB / ID: 3ubr
TitleLaue structure of Shewanella oneidensis cytochrome-c Nitrite Reductase
ComponentsCytochrome c-552
KeywordsOXIDOREDUCTASE / deca-heme / electron transfer / redox / CymA
Function / homology
Function and homology information


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 / 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
HEME C / Cytochrome c-552
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsYoungblut, M. / Judd, E.T. / Srajer, V. / Sayed, B. / Goeltzner, T. / Elliott, S. / Schmidt, M. / Pacheco, A.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2012
Title: Laue crystal structure of Shewanella oneidensis cytochrome c nitrite reductase from a high-yield expression system.
Authors: Youngblut, M. / Judd, E.T. / Srajer, V. / Sayyed, B. / Goelzer, T. / Elliott, S.J. / Schmidt, M. / Pacheco, A.A.
History
DepositionOct 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Mar 15, 2017Group: Other
Revision 1.3Sep 4, 2019Group: Data collection / Derived calculations / Category: reflns / struct_conn
Item: _reflns.pdbx_Rsym_value / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Sep 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_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.conn_type_id / _struct_conn.id / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c-552
B: Cytochrome c-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,40014
Polymers99,1352
Non-polymers6,26512
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16110 Å2
ΔGint-259 kcal/mol
Surface area34400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.500, 95.900, 223.800
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-552 / Ammonia-forming cytochrome c nitrite reductase / Cytochrome c nitrite reductase


Mass: 49567.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: nrfA, Shewanella oneidensis, SO_3980 / Production host: Shewanella (bacteria)
References: UniProt: Q8EAC7, nitrite reductase (cytochrome; ammonia-forming)
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: 14% PEG 4K, pH 8.25, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.05-1.15
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 17, 2011
RadiationMonochromator: no monochromator / Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.051
21.151
ReflectionResolution: 2.59→100 Å / Num. all: 25875 / Num. obs: 25875 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 16.7
Reflection shellResolution: 2.59→2.72 Å / Redundancy: 7.6 % / % possible all: 40.5

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Processing

Software
NameVersionClassification
LaueCollectdata collection
PHASERphasing
REFMAC5.5.0109refinement
Precognitiondata reduction
Epinormdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RDZ

2rdz


Resolution: 2.59→40.56 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.821 / SU B: 14.737 / SU ML: 0.305 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28462 1315 5.1 %RANDOM
Rwork0.19024 ---
all0.195 24561 --
obs0.195 24561 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.071 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.59→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6946 0 432 155 7533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227616
X-RAY DIFFRACTIONr_bond_other_d0.0010.025104
X-RAY DIFFRACTIONr_angle_refined_deg1.5312.12610422
X-RAY DIFFRACTIONr_angle_other_deg0.945312466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0625876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97324.875320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.008151292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8931530
X-RAY DIFFRACTIONr_chiral_restr0.0810.21004
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218424
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021400
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_it0.4631.54384
X-RAY DIFFRACTIONr_mcbond_other0.0671.51758
X-RAY DIFFRACTIONr_mcangle_it0.86227040
X-RAY DIFFRACTIONr_scbond_it1.09533232
X-RAY DIFFRACTIONr_scangle_it1.7844.53382
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.59→2.657 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.438 44 -
Rwork0.312 690 -
obs--100 %

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