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- PDB-3lg1: Structure of the Thioalkalivibrio nitratireducens cytochrome c ni... -

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Basic information

Entry
Database: PDB / ID: 3lg1
TitleStructure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase reduced by sodium borohydride (in complex with sulfite)
ComponentsEight-heme nitrite reductase
KeywordsOXIDOREDUCTASE / alpha protein / eight hemes c
Function / homology
Function and homology information


ammonium ion metabolic process / nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / anaerobic electron transport chain / nitrate assimilation / outer membrane-bounded periplasmic space / calcium ion binding / heme binding
Similarity search - Function
Helix Hairpins - #3080 / 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 / Helix Hairpins ...Helix Hairpins - #3080 / 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 / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Chem-PG6 / SULFITE ION / Cytochrome c-552 / Cytochrome c-552
Similarity search - Component
Biological speciesThioalkalivibrio nitratireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsTrofimov, A.A. / Polyakov, K.M. / Boyko, K.M. / Filimonenkov, A.A. / Dorovatovsky, P.V. / Tikhonova, T.V. / Popov, V.O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Covalent modifications of the catalytic tyrosine in octahaem cytochrome c nitrite reductase and their effect on the enzyme activity.
Authors: Trofimov, A.A. / Polyakov, K.M. / Tikhonova, T.V. / Tikhonov, A.V. / Safonova, T.N. / Boyko, K.M. / Dorovatovskii, P.V. / Popov, V.O.
History
DepositionJan 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 15, 2012Group: Database references
Revision 1.3Sep 6, 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_struct_special_symmetry / 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_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.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: Eight-heme nitrite reductase
B: Eight-heme nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,76157
Polymers118,9832
Non-polymers15,77955
Water17,547974
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)404,284171
Polymers356,9486
Non-polymers47,336165
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Unit cell
Length a, b, c (Å)192.620, 192.620, 192.620
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-531-

NA

21A-537-

SO3

31B-530-

NA

41B-533-

SO3

51B-536-

SO3

61A-986-

HOH

71A-1014-

HOH

81B-1010-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Eight-heme nitrite reductase


Mass: 59491.309 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thioalkalivibrio nitratireducens (bacteria)
Strain: ALEN 2 / References: UniProt: Q5F2I3, UniProt: L0DSL2*PLUS

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Non-polymers , 7 types, 1029 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.: 5 / Source method: obtained synthetically / Formula: SO3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C12H26O6
#7: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 974 / 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: 4.18 Å3/Da / Density % sol: 70.35 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: Protein solution (2.5mcl): 9.3mg/ml TvNiR, 0.1M potassium phosphate (pH7.0). Reservoir solution (2.5mcl): 0.2M tri-sodium citrate dihydrate, 0.1M Tris hydrochloride (pH8.5), 30% v/v PEG 400. ...Details: Protein solution (2.5mcl): 9.3mg/ml TvNiR, 0.1M potassium phosphate (pH7.0). Reservoir solution (2.5mcl): 0.2M tri-sodium citrate dihydrate, 0.1M Tris hydrochloride (pH8.5), 30% v/v PEG 400. Crystals were soaked in 0.08M sodium sulfite, 0.13M sodium borohydride, 0.02M methyl viologen solution for 10min, pH 8.7, 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: 0.9886 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9886 Å / Relative weight: 1
ReflectionResolution: 1.95→19.9 Å / Num. all: 171816 / Num. obs: 171512 / % possible obs: 99.7 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.144 / Net I/σ(I): 12.43
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 2.85 / Num. unique all: 12457 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FO3

3fo3


Resolution: 1.95→19.9 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.025 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1826 8611 5 %RANDOM
Rwork0.16068 ---
obs0.16178 162890 99.68 %-
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: 20.984 Å2
Refine analyzeLuzzati coordinate error obs: 0.181 Å
Refinement stepCycle: LAST / Resolution: 1.95→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8212 0 912 974 10098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0219592
X-RAY DIFFRACTIONr_angle_refined_deg1.542.15413030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14351036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49923.843458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.965151372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3081562
X-RAY DIFFRACTIONr_chiral_restr0.1030.21203
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0217426
X-RAY DIFFRACTIONr_mcbond_it0.7351.55181
X-RAY DIFFRACTIONr_mcangle_it1.30428316
X-RAY DIFFRACTIONr_scbond_it2.04534411
X-RAY DIFFRACTIONr_scangle_it3.0594.54714
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 654 -
Rwork0.216 11949 -
obs--99.9 %

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