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

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Basic information

Entry
Database: PDB / ID: 3lgq
TitleStructure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with sulfite (modified Tyr-303)
ComponentsEight-heme nitrite reductase
KeywordsOXIDOREDUCTASE / alpha protein / eight hemes c
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 / heme binding / calcium ion 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 / SULFITE ION / Cytochrome c-552 / Cytochrome c-552
Similarity search - Component
Biological speciesThioalkalivibrio nitratireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTrofimov, A.A. / Polyakov, K.M. / Boyko, K.M. / Filimonenkov, A.A. / Tikhonova, T.V. / Lamzin, V.S. / Bourenkov, G.P. / 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 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 15, 2012Group: Database references
Revision 1.3Sep 6, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / 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_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 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: Eight-heme nitrite reductase
B: Eight-heme nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,84029
Polymers118,9832
Non-polymers10,85727
Water20,5371140
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)389,51987
Polymers356,9486
Non-polymers32,57181
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 area95230 Å2
ΔGint-1301 kcal/mol
Surface area96140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.690, 195.690, 195.690
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-530-

TRS

21A-530-

TRS

31B-531-

TRS

41B-531-

TRS

51A-564-

HOH

61A-565-

HOH

71A-593-

HOH

81A-1016-

HOH

91B-594-

HOH

101B-1082-

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 , 6 types, 1167 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.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1140 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.36 Å3/Da / Density % sol: 71.54 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein solution (2.5mcl): 10mg/ml TvNiR, 0.05M Tris hydrochloride (pH7.2). Reservoir solution (2.5mcl): 0.2M ammonium acetate, 0.1M tri-sodium citrate dihydrate, 30% v/v 2-methyl-2,4- ...Details: Protein solution (2.5mcl): 10mg/ml TvNiR, 0.05M Tris hydrochloride (pH7.2). Reservoir solution (2.5mcl): 0.2M ammonium acetate, 0.1M tri-sodium citrate dihydrate, 30% v/v 2-methyl-2,4-pentanediol, 0.1M sodium sulfite (pH6.5), 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: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 30, 2009
RadiationMonochromator: Si(111), horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.8→19.8 Å / Num. all: 228946 / Num. obs: 221170 / % possible obs: 96.6 % / Redundancy: 3 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.1
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.1 / Num. unique all: 17909 / % possible all: 73.1

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Processing

Software
NameVersionClassification
DNAdata collection
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GM6

3gm6


Resolution: 1.8→19.8 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.435 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1675 11090 5 %RANDOM
Rwork0.15048 ---
obs0.15134 210080 97.62 %-
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: 25.163 Å2
Refine analyzeLuzzati coordinate error obs: 0.167 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8232 0 742 1140 10114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0219501
X-RAY DIFFRACTIONr_angle_refined_deg1.472.14512998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0951038
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66923.833467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.065151405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7341565
X-RAY DIFFRACTIONr_chiral_restr0.1070.21219
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0217457
X-RAY DIFFRACTIONr_mcbond_it0.6881.55198
X-RAY DIFFRACTIONr_mcangle_it1.2628372
X-RAY DIFFRACTIONr_scbond_it2.00634303
X-RAY DIFFRACTIONr_scangle_it3.1124.54626
LS refinement shellResolution: 1.806→1.853 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 712 -
Rwork0.231 13463 -
obs--85.25 %

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