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- PDB-8bcx: Crystal structure of NrfA-1 from Geobacter metallireducens -

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Basic information

Entry
Database: PDB / ID: 8bcx
TitleCrystal structure of NrfA-1 from Geobacter metallireducens
ComponentsNitrite reductase (cytochrome; ammonia-forming)
KeywordsOXIDOREDUCTASE / Nitrite reductase / cytochrome c / dissimilatory nitrate reduction to ammonium (DNRA)
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 metallireducens GS-15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.941 Å
AuthorsDenkhaus, L. / Siffert, F. / Einsle, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Fems Microbiol.Lett. / Year: 2023
Title: An unusual active site architecture in cytochrome c nitrite reductase NrfA-1 from Geobacter metallireducens.
Authors: Denkhaus, L. / Siffert, F. / Einsle, O.
History
DepositionOct 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,01938
Polymers220,3054
Non-polymers13,71534
Water13,061725
1
A: Nitrite reductase (cytochrome; ammonia-forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4579
Polymers55,0761
Non-polymers3,3818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nitrite reductase (cytochrome; ammonia-forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,55310
Polymers55,0761
Non-polymers3,4779
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nitrite reductase (cytochrome; ammonia-forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4579
Polymers55,0761
Non-polymers3,3818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nitrite reductase (cytochrome; ammonia-forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,55310
Polymers55,0761
Non-polymers3,4779
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.085, 91.965, 123.939
Angle α, β, γ (deg.)90, 99.06, 90
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 55076.129 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens GS-15 (bacteria)
Strain: ATCC 53774 / DSM 7210 / GS-15 / Gene: nrfA-1, Gmet_0294 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43
References: UniProt: Q39YY5, nitrite reductase (cytochrome; ammonia-forming)
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 725 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M BIS-TRIS pH 5.5, 0.1 M ammonium sulfate, 22.5 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.734 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.734 Å / Relative weight: 1
ReflectionResolution: 1.94→122.39 Å / Num. obs: 92671 / % possible obs: 62.1 % / Redundancy: 53.5 % / CC1/2: 0.999 / Net I/σ(I): 13.5
Reflection shellResolution: 1.94→2.17 Å / Num. unique obs: 4634 / CC1/2: 0.855

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (8-JUN-2022)refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.941→122.39 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.31 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.307 / SU Rfree Blow DPI: 0.207 / SU Rfree Cruickshank DPI: 0.21
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 4540 -RANDOM
Rwork0.1928 ---
obs0.1945 92671 62.1 %-
Displacement parametersBiso mean: 35.59 Å2
Baniso -1Baniso -2Baniso -3
1--2.9928 Å20 Å2-0.2822 Å2
2--5.9416 Å20 Å2
3----2.9488 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.941→122.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13813 0 930 725 15468
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00815218HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8720592HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5418SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes3138HARMONIC5
X-RAY DIFFRACTIONt_it15218HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1812SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact12116SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion15.87
LS refinement shellResolution: 1.941→2.11 Å
RfactorNum. reflection% reflection
Rfree0.2585 96 -
Rwork0.2686 --
obs--5.5 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7681-0.1154-0.25140.9071-0.08341.4463-0.0358-0.20450.1595-0.20450.04630.12330.15950.1233-0.0106-0.08420.0442-0.0085-0.0066-0.0164-0.104634.560421.612530.3008
22.2942-0.6118-1.16381.15180.6122.16650.182-0.2727-0.2568-0.2727-0.02840.286-0.25680.286-0.1535-0.1106-0.00410.02780.0260.007-0.095433.210367.642439.9222
30.63040.0415-0.0650.3763-0.15584.595-0.0312-0.13870.1226-0.13870.0165-0.77480.1226-0.77480.0148-0.0998-0.0087-0.00430.0869-0.0015-0.1274-7.905231.552523.6956
40.8944-0.07210.58160.3316-0.22933.80080.0355-0.09670.0029-0.0967-0.0124-0.53420.0029-0.5342-0.0231-0.09190.0418-0.0010.006-0.0073-0.0964-8.8319-14.711833.529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A39 - 488
2X-RAY DIFFRACTION1{ A|* }A501 - 505
3X-RAY DIFFRACTION2{ B|* }B38 - 488
4X-RAY DIFFRACTION2{ B|* }B501 - 505
5X-RAY DIFFRACTION3{ C|* }C34 - 488
6X-RAY DIFFRACTION3{ C|* }C501 - 505
7X-RAY DIFFRACTION4{ D|* }D34 - 488
8X-RAY DIFFRACTION4{ D|* }D501 - 505

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