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- PDB-6v0a: Crystal structure of cytochrome c nitrite reductase from the bact... -

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Basic information

Entry
Database: PDB / ID: 6v0a
TitleCrystal structure of cytochrome c nitrite reductase from the bacterium Geobacter lovleyi with bound sulfate
ComponentsNitrite reductase (cytochrome; ammonia-forming)
KeywordsOXIDOREDUCTASE / Ammonia-forming / cytochrome 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
Cytochrome c552 / Cytochrome c552 / Multiheme cytochrome superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
HEME C / nitrite reductase (cytochrome; ammonia-forming)
Similarity search - Component
Biological speciesGeobacter lovleyi
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSatyanarayana, L. / Campecino, J. / Hegg, L.H. / Hu, J.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Cytochromecnitrite reductase from the bacteriumGeobacter lovleyirepresents a new NrfA subclass.
Authors: Campecino, J. / Lagishetty, S. / Wawrzak, Z. / Sosa Alfaro, V. / Lehnert, N. / Reguera, G. / Hu, J. / Hegg, E.L.
History
DepositionNov 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _struct.title
Revision 1.2Sep 2, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_conn_type
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _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_type.id
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrite reductase (cytochrome; ammonia-forming)
B: Nitrite reductase (cytochrome; ammonia-forming)
C: Nitrite reductase (cytochrome; ammonia-forming)
D: Nitrite reductase (cytochrome; ammonia-forming)
E: Nitrite reductase (cytochrome; ammonia-forming)
F: Nitrite reductase (cytochrome; ammonia-forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,96842
Polymers325,8376
Non-polymers19,13136
Water16,123895
1
A: Nitrite reductase (cytochrome; ammonia-forming)
B: Nitrite reductase (cytochrome; ammonia-forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,98914
Polymers108,6122
Non-polymers6,37712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16040 Å2
ΔGint-275 kcal/mol
Surface area32390 Å2
MethodPISA
2
C: Nitrite reductase (cytochrome; ammonia-forming)
D: Nitrite reductase (cytochrome; ammonia-forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,98914
Polymers108,6122
Non-polymers6,37712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16000 Å2
ΔGint-278 kcal/mol
Surface area32180 Å2
MethodPISA
3
E: Nitrite reductase (cytochrome; ammonia-forming)
F: Nitrite reductase (cytochrome; ammonia-forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,98914
Polymers108,6122
Non-polymers6,37712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15950 Å2
ΔGint-276 kcal/mol
Surface area32260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.859, 144.616, 234.887
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 35 through 77 or resid 79...
21(chain B and (resid 35 through 77 or resid 79...
31(chain C and (resid 35 through 77 or resid 79...
41(chain D and (resid 35 through 77 or resid 79...
51(chain E and (resid 35 through 161 or resid 163...
61(chain F and (resid 35 through 77 or resid 79...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 35 through 77 or resid 79...A35 - 77
121(chain A and (resid 35 through 77 or resid 79...A79 - 161
131(chain A and (resid 35 through 77 or resid 79...A163 - 305
141(chain A and (resid 35 through 77 or resid 79...A308 - 310
151(chain A and (resid 35 through 77 or resid 79...A457 - 478
161(chain A and (resid 35 through 77 or resid 79...A537 - 541
171(chain A and (resid 35 through 77 or resid 79...A1523
211(chain B and (resid 35 through 77 or resid 79...B35 - 77
221(chain B and (resid 35 through 77 or resid 79...B79 - 161
231(chain B and (resid 35 through 77 or resid 79...B163 - 202
241(chain B and (resid 35 through 77 or resid 79...B35 - 541
251(chain B and (resid 35 through 77 or resid 79...B312 - 325
261(chain B and (resid 35 through 77 or resid 79...B457 - 475
271(chain B and (resid 35 through 77 or resid 79...B457 - 478
281(chain B and (resid 35 through 77 or resid 79...B537 - 541
291(chain B and (resid 35 through 77 or resid 79...B1523
311(chain C and (resid 35 through 77 or resid 79...C35 - 77
321(chain C and (resid 35 through 77 or resid 79...C79 - 202
331(chain C and (resid 35 through 77 or resid 79...C204 - 305
341(chain C and (resid 35 through 77 or resid 79...C308 - 310
351(chain C and (resid 35 through 77 or resid 79...C35 - 541
361(chain C and (resid 35 through 77 or resid 79...C327 - 455
371(chain C and (resid 35 through 77 or resid 79...C457 - 541
381(chain C and (resid 35 through 77 or resid 79...C1523
411(chain D and (resid 35 through 77 or resid 79...D35 - 77
421(chain D and (resid 35 through 77 or resid 79...D79 - 161
431(chain D and (resid 35 through 77 or resid 79...D163 - 202
441(chain D and (resid 35 through 77 or resid 79...D327 - 455
451(chain D and (resid 35 through 77 or resid 79...D35 - 541
461(chain D and (resid 35 through 77 or resid 79...D537 - 541
471(chain D and (resid 35 through 77 or resid 79...D35 - 541
481(chain D and (resid 35 through 77 or resid 79...D537 - 541
491(chain D and (resid 35 through 77 or resid 79...D1523
511(chain E and (resid 35 through 161 or resid 163...E35 - 161
521(chain E and (resid 35 through 161 or resid 163...E163 - 202
531(chain E and (resid 35 through 161 or resid 163...E204 - 305
541(chain E and (resid 35 through 161 or resid 163...E308 - 310
551(chain E and (resid 35 through 161 or resid 163...E327 - 478
561(chain E and (resid 35 through 161 or resid 163...E537 - 1523
611(chain F and (resid 35 through 77 or resid 79...F35 - 77
621(chain F and (resid 35 through 77 or resid 79...F79 - 305
631(chain F and (resid 35 through 77 or resid 79...F308 - 325
641(chain F and (resid 35 through 77 or resid 79...F35 - 478
651(chain F and (resid 35 through 77 or resid 79...F457 - 478
661(chain F and (resid 35 through 77 or resid 79...F537 - 1523

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Components

#1: Protein
Nitrite reductase (cytochrome; ammonia-forming)


Mass: 54306.129 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter lovleyi (strain ATCC BAA-1151 / DSM 17278 / SZ) (bacteria)
Strain: ATCC BAA-1151 / DSM 17278 / SZ / Cell line: SZ / Gene: Glov_1042 / Variant: DSM 17278 / Plasmid: D-TOPO 45 / Details (production host): pBAD202/D-TOPO 45 / Production host: Shewanella oneidensis MR-1 (bacteria) / Strain (production host): MR-1
References: UniProt: B3E641, nitrite reductase (cytochrome; ammonia-forming)
#2: Chemical...
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 895 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.3 Å3/Da / Density % sol: 58 %
Description: Initial crystal appeared after a week consisting of thin long needle clusters, a reddish brown micro-crystals. The crystallization hit condition were further optimized by changing the ...Description: Initial crystal appeared after a week consisting of thin long needle clusters, a reddish brown micro-crystals. The crystallization hit condition were further optimized by changing the various parameters of crystallization hit condition starting from pH, precipitant and protein concentration in corning 48 three well plate to obtained thick long needle like crystals.
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% (w/v) PEG 3350 and 200 mM Sodium Malonate as precipitant and protein concentration 10 mg/ml in 150 mM NaCl, 30 mM Ammonium Sulphate and 10 mM Hepes buffer pH 7.0
PH range: 6.0-7.5
Temp details: Crystal were grown at 8 degree centigrade, a cold room temperature

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen cryogenic condition / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.722 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 21, 2019 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.722 Å / Relative weight: 1
ReflectionResolution: 2.549→30 Å / Num. obs: 122318 / % possible obs: 99 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.109 / Rrim(I) all: 0.262 / Χ2: 1.563 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.595.31.65560920.350.7671.81.01799.6
2.59-2.645.31.42460980.3960.661.51.02999.6
2.64-2.695.31.23260260.4930.5690.131.03999.6
2.69-2.755.31.07260840.5730.4961.1851.07399.4
2.75-2.815.30.90560690.6540.4190.11.09799.2
2.81-2.875.30.82160510.6820.3810.9081.14499
2.87-2.945.20.71261020.7510.3340.7891.17599.2
2.94-3.025.30.61660480.7960.2870.6811.20199
3.02-3.115.20.52260320.8340.2480.5791.2698.7
3.11-3.214.50.40160110.8760.2060.4531.30697.6
3.21-3.334.20.32459200.9010.1690.3671.37496.6
3.33-3.465.70.28461400.950.1280.3121.45599.6
3.46-3.6260.22561240.970.0990.2471.51199.7
3.62-3.8160.17961790.9780.0790.1961.62699.8
3.81-4.0560.14661550.9860.0640.161.73299.8
4.05-4.365.90.11761790.9910.0520.1281.8799.8
4.36-4.7960.10162280.9920.0450.1112.003100
4.79-5.485.40.161690.9920.0470.1112.14598.8
5.48-6.95.10.09760660.9920.0460.1072.32195.9
6.9-106.90.06765450.9970.0270.0722.982100

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Processing

Software
NameVersionClassification
PHENIX1.15.1_3469refinement
SCALEPACKHKL200data scaling
PDB_EXTRACT3.25data extraction
DENZOHKL2000data reduction
MrBUMPCCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FE anomalous signal at 1.7 A build model

Resolution: 2.55→29.664 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.31
RfactorNum. reflection% reflection
Rfree0.242 6074 4.97 %
Rwork0.1883 --
obs0.191 122200 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.98 Å2 / Biso mean: 39.061 Å2 / Biso min: 11.96 Å2
Refinement stepCycle: final / Resolution: 2.55→29.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21161 0 1320 895 23376
Biso mean--31.71 33.91 -
Num. residues----2657
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8001X-RAY DIFFRACTION5.782TORSIONAL
12B8001X-RAY DIFFRACTION5.782TORSIONAL
13C8001X-RAY DIFFRACTION5.782TORSIONAL
14D8001X-RAY DIFFRACTION5.782TORSIONAL
15E8001X-RAY DIFFRACTION5.782TORSIONAL
16F8001X-RAY DIFFRACTION5.782TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.55-2.57810.38591790.3243381997
2.5781-2.60840.33241940.3053831100
2.6084-2.64020.35151790.28553909100
2.6402-2.67360.3281670.28143835100
2.6736-2.70870.34651970.27173862100
2.7087-2.74580.34092220.271381899
2.7458-2.7850.31891790.2629389699
2.785-2.82650.34982010.2651381099
2.8265-2.87070.30482120.2512383599
2.8707-2.91770.32572060.2416385699
2.9177-2.9680.28061970.2355382499
2.968-3.02190.30471970.2294384699
3.0219-3.07990.28092010.2259388699
3.0799-3.14270.28982060.2233378098
3.1427-3.2110.30231970.223377497
3.211-3.28560.28372180.2107370095
3.2856-3.36760.28062090.2038388399
3.3676-3.45860.25962170.19463852100
3.4586-3.56020.25961980.18423883100
3.5602-3.67490.26072300.18233886100
3.6749-3.8060.21962040.17423900100
3.806-3.9580.221990.15893915100
3.958-4.13770.21242310.14893884100
4.1377-4.35520.18162150.13913892100
4.3552-4.62710.15952070.13433940100
4.6271-4.98290.18742100.13063942100
4.9829-5.48150.16591900.1403390299
5.4815-6.26810.19181990.1545374894
6.2681-7.87270.19162060.15064038100
7.8727-29.660.16362070.1434180100

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