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- PDB-4l3z: Nitrite complex of TvNiR, second middle dose data set -

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Basic information

Entry
Database: PDB / ID: 4l3z
TitleNitrite complex of TvNiR, second middle dose data set
ComponentsEight-heme nitrite reductase
KeywordsOXIDOREDUCTASE / 8 hemes c
Function / homology
Function and homology information


ammonium ion metabolic process / nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / nitrate assimilation / 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 / NITRITE ION / Cytochrome c-552
Similarity search - Component
Biological speciesThioalkalivibrio nitratireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsTrofimov, A.A. / Polyakov, K.M. / Lazarenko, V.A. / Popov, A.N. / Tikhonova, T.V. / Tikhonov, A.V. / Popov, V.O.
CitationJournal: To be Published
Title: Investigation of the X-ray-induced nitrite reduction catalysed by cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens
Authors: Trofimov, A.A. / Polyakov, K.M. / Lazarenko, V.A. / Popov, A.N. / Tikhonova, T.V. / Tikhonov, A.V. / Popov, V.O.
History
DepositionJun 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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.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_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.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.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_ref_seq_dif.details / _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)129,08937
Polymers117,8682
Non-polymers11,22135
Water22,1401229
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)387,267111
Polymers353,6036
Non-polymers33,664105
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 area99880 Å2
ΔGint-1460 kcal/mol
Surface area95760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.920, 194.920, 194.920
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-1036-

HOH

21A-1220-

HOH

31A-1280-

HOH

41A-1283-

HOH

51B-1062-

HOH

61B-1066-

HOH

71B-1310-

HOH

81B-1317-

HOH

91B-1318-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Eight-heme nitrite reductase


Mass: 58933.777 Da / Num. of mol.: 2 / Fragment: unp residues 33-551 / Source method: isolated from a natural source
Source: (natural) Thioalkalivibrio nitratireducens (bacteria)
Strain: DSM 14787 / UNIQEM 213 / ALEN2
References: UniProt: L0DSL2, nitrite reductase (cytochrome; ammonia-forming)

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Non-polymers , 7 types, 1264 molecules

#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / 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-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.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1229 / 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: 5.24 Å3/Da / Density % sol: 76.51 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution (2.5mcl): 10.0 mg/ml TvNiR, 0.05M Tris-HCl, pH7.2. Reservoir solution (2.5mcl): 1.26M tri-sodium citrate dihydrate, 0.09M HEPES/NaOH, 10% v/v glycerol, pH 7.5, VAPOR ...Details: Protein solution (2.5mcl): 10.0 mg/ml TvNiR, 0.05M Tris-HCl, pH7.2. Reservoir solution (2.5mcl): 1.26M tri-sodium citrate dihydrate, 0.09M HEPES/NaOH, 10% v/v glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.85→29.07 Å / Num. all: 207965 / Num. obs: 207965 / % possible obs: 99.4 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 8.3
Reflection shellResolution: 1.85→1.9 Å / Rmerge(I) obs: 0.803 / Mean I/σ(I) obs: 1.9 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementResolution: 1.85→29.07 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.668 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1741 10424 5 %RANDOM
Rwork0.15548 ---
obs0.15642 196749 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.372 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8258 0 757 1229 10244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0199512
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5782.02213008
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08251038
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07323.894470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81151381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3881564
X-RAY DIFFRACTIONr_chiral_restr0.1130.21233
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0217541
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 786 -
Rwork0.271 14320 -
obs--98.96 %

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