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- PDB-3f29: Structure of the Thioalkalivibrio nitratireducens cytochrome c ni... -

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Basic information

Entry
Database: PDB / ID: 3f29
TitleStructure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase 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: 2 Å
AuthorsTrofimov, A.A. / Polyakov, K.M. / Boyko, K.M. / Slutsky, A. / Tikhonova, T.V. / Antipov, A.N. / Zvyagilskaya, R.A. / Popov, A.N. / Lamzin, V.S. / Bourenkov, G.P. / Popov, V.O.
CitationJournal: To be Published
Title: Binding of sulfite by the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase
Authors: Trofimov, A.A. / Polyakov, K.M. / Tikhonova, T.V. / Popov, V.O.
History
DepositionOct 29, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 22, 2014Group: Derived calculations
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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)132,21539
Polymers118,9832
Non-polymers13,23237
Water19,5641086
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)396,644117
Polymers356,9486
Non-polymers39,696111
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
Buried area99700 Å2
ΔGint-1133.2 kcal/mol
Surface area97530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.568, 193.568, 193.568
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
11B-529-

SO3

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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 , 6 types, 1123 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.: 3 / 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-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26O6
#6: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1086 / 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: 4.23 Å3/Da / Density % sol: 70.07 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: Protein solution (5mcl): 14.5mg/ml TvNiR, 0.005M Tris borate (pH8.7), Reservoir solution (5mcl): 0.2M tri-sodium citrate dihydrate, 0.1M Tris hydrochloride (pH8.5), 30% PEG 400, VAPOR ...Details: Protein solution (5mcl): 14.5mg/ml TvNiR, 0.005M Tris borate (pH8.7), Reservoir solution (5mcl): 0.2M tri-sodium citrate dihydrate, 0.1M Tris hydrochloride (pH8.5), 30% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 24, 2005
RadiationMonochromator: Si(111), horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 192707 / Num. obs: 157823 / % possible obs: 97.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.5
Reflection shellResolution: 2.02→2.08 Å / Rmerge(I) obs: 0.062 / Mean I/σ(I) obs: 13.3 / % possible all: 97.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.97 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17395 8007 -RANDOM
Rwork0.15375 ---
obs0.15476 149777 97.48 %-
Displacement parametersBiso mean: 21.599 Å2
Refine analyzeLuzzati coordinate error obs: 0.179 Å
Refinement stepCycle: LAST / Resolution: 2→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8204 0 795 1086 10085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0219520
X-RAY DIFFRACTIONr_angle_refined_deg1.2592.14712984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87551041
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7123.939462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.661151384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5031561
X-RAY DIFFRACTIONr_chiral_restr0.0820.21212
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027445
X-RAY DIFFRACTIONr_nbd_refined0.1990.24708
X-RAY DIFFRACTIONr_nbtor_refined0.2940.26424
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.21006
X-RAY DIFFRACTIONr_metal_ion_refined0.0480.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.2118
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0840.257
X-RAY DIFFRACTIONr_mcbond_it0.621.55338
X-RAY DIFFRACTIONr_mcangle_it1.00828359
X-RAY DIFFRACTIONr_scbond_it1.57334960
X-RAY DIFFRACTIONr_scangle_it2.3164.54593
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 566 -
Rwork0.172 10980 -
obs--97.02 %

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