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- PDB-3ttb: Structure of the Thioalkalivibrio paradoxus cytochrome c nitrite ... -

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Basic information

Entry
Database: PDB / ID: 3ttb
TitleStructure of the Thioalkalivibrio paradoxus cytochrome c nitrite reductase in complex with sulfite
ComponentsEight-heme nitrite reductase
KeywordsOXIDOREDUCTASE / eight hemes c / nitrite reductase
Function / homology
Function and homology information


nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / periplasmic space / metal ion binding
Similarity search - Function
Helix Hairpins - #3080 / Cytochrome c552 / Cytochrome c552 / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Multiheme cytochrome superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Helix Hairpins / Up-down Bundle ...Helix Hairpins - #3080 / Cytochrome c552 / Cytochrome c552 / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Multiheme cytochrome superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / HEME C / SULFITE ION / nitrite reductase (cytochrome; ammonia-forming)
Similarity search - Component
Biological speciesThioalkalivibrio paradoxus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPolyakov, K.M. / Trofimov, A.A. / Tikhonova, T.V. / Tikhonov, A.V. / Dorovatovskii, P.V. / Popov, V.O.
CitationJournal: Febs J. / Year: 2012
Title: Comparative structural and functional analysis of two octaheme nitrite reductases from closely related Thioalkalivibrio species.
Authors: Tikhonova, T. / Tikhonov, A. / Trofimov, A. / Polyakov, K. / Boyko, K. / Cherkashin, E. / Rakitina, T. / Sorokin, D. / Popov, V.
History
DepositionSep 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Dec 19, 2012Group: Database references
Revision 1.3Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
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_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.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.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_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: Eight-heme nitrite reductase
B: Eight-heme nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,96338
Polymers118,4582
Non-polymers11,50536
Water13,259736
1
A: Eight-heme nitrite reductase
B: Eight-heme nitrite reductase
hetero molecules

A: Eight-heme nitrite reductase
B: Eight-heme nitrite reductase
hetero molecules

A: Eight-heme nitrite reductase
B: Eight-heme nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)389,889114
Polymers355,3746
Non-polymers34,515108
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)190.990, 190.990, 190.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-561-

HOH

21A-817-

HOH

31A-818-

HOH

41A-879-

HOH

51B-538-

HOH

61B-539-

HOH

71B-557-

HOH

81B-569-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Eight-heme nitrite reductase


Mass: 59228.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thioalkalivibrio paradoxus (bacteria) / Strain: ARh1 / References: UniProt: E7EDQ7

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Non-polymers , 7 types, 772 molecules

#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 736 / 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: 4.94 Å3/Da / Density % sol: 75.08 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein solution (2.5mcl): 10mg/ml TvPaR, 0.05M Tris-HCl, pH8.0. Reservoir solution (2.5mcl): 0.02M cobalt chloride, 0.1M MES (pH 6.5), 1.8 M ammonium sulfate. The crystal was soaked in 0. ...Details: Protein solution (2.5mcl): 10mg/ml TvPaR, 0.05M Tris-HCl, pH8.0. Reservoir solution (2.5mcl): 0.02M cobalt chloride, 0.1M MES (pH 6.5), 1.8 M ammonium sulfate. The crystal was soaked in 0.05M sodium dithionite for 5 days, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.9779 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.489
11-H, L, K20.511
ReflectionResolution: 2→39 Å / Num. all: 155579 / Num. obs: 155516 / % possible obs: 100 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 16.53
Reflection shellResolution: 2→2.2 Å / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 3.94 / Num. unique all: 38451 / % possible all: 100

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Processing

Software
NameVersionClassification
AUTOMARdata collection
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SXQ

3sxq


Resolution: 2→38.99 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.079 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.017 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.15298 7717 5 %RANDOM
Rwork0.1341 ---
obs0.13505 147798 99.96 %-
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: 22.994 Å2
Refine analyzeLuzzati coordinate error obs: 0.134 Å
Refinement stepCycle: LAST / Resolution: 2→38.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8204 0 759 736 9699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0219395
X-RAY DIFFRACTIONr_angle_refined_deg1.6992.14812875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67451036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92923.544443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.986151316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3281562
X-RAY DIFFRACTIONr_chiral_restr0.1050.21207
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0217386
X-RAY DIFFRACTIONr_mcbond_it0.41.25186
X-RAY DIFFRACTIONr_mcangle_it0.7061.58334
X-RAY DIFFRACTIONr_scbond_it0.6651.54209
X-RAY DIFFRACTIONr_scangle_it0.96924541
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 585 -
Rwork0.277 10855 -
obs--99.96 %

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