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- PDB-6tpo: Conformation of cd1 nitrite reductase NirS without bound heme d1 -

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Basic information

Entry
Database: PDB / ID: 6tpo
TitleConformation of cd1 nitrite reductase NirS without bound heme d1
ComponentsNitrite reductase
KeywordsOXIDOREDUCTASE / cd1 nitrite reductase / NirS
Function / homology
Function and homology information


hydroxylamine reductase / hydroxylamine reductase activity / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / periplasmic space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome cd1-nitrite reductase, C-terminal domain superfamily / Cytochrome D1 heme domain / : / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
(R,R)-2,3-BUTANEDIOL / HEME C / Nitrite reductase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.861 Å
AuthorsKluenemann, T. / Blankenfeldt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK2223/1 Germany
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Structure of heme d 1 -free cd 1 nitrite reductase NirS.
Authors: Klunemann, T. / Blankenfeldt, W.
History
DepositionDec 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 1.2Nov 6, 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

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Assembly

Deposited unit
A: Nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2064
Polymers60,2591
Non-polymers9473
Water4,594255
1
A: Nitrite reductase
hetero molecules

A: Nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,4128
Polymers120,5182
Non-polymers1,8946
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/41
Unit cell
Length a, b, c (Å)67.245, 67.245, 277.104
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-1060-

HOH

21A-1105-

HOH

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Components

#1: Protein Nitrite reductase / Cytochrome cd1 / Cytochrome oxidase / Hydroxylamine reductase


Mass: 60259.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
References: UniProt: P24474, nitrite reductase (NO-forming), hydroxylamine reductase
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 0.1M Phosphate/citrate pH4.2 40% (v/v) PEG300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.033217 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033217 Å / Relative weight: 1
ReflectionResolution: 1.86→69.28 Å / Num. obs: 54867 / % possible obs: 100 % / Redundancy: 24 % / CC1/2: 0.997 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.033 / Rrim(I) all: 0.16 / Net I/σ(I): 18 / Num. measured all: 1316645 / Scaling rejects: 44
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.86-1.9618.71.40614646578120.8060.3261.4442.8
5.88-69.2822.40.0914528920250.9890.020.09443.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.1data scaling
PHENIXdev-3714refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
autoPROCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1hzu

1hzu


Resolution: 1.861→54.364 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.84
RfactorNum. reflection% reflection
Rfree0.1937 2726 4.98 %
Rwork0.1663 --
obs0.1677 54747 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.22 Å2 / Biso mean: 34.4895 Å2 / Biso min: 14.63 Å2
Refinement stepCycle: final / Resolution: 1.861→54.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4071 0 127 255 4453
Biso mean--45.93 34.46 -
Num. residues----523
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.861-1.89430.24691450.22092647
1.8943-1.93080.25611130.20392738
1.9308-1.97020.20561340.1822690
1.9702-2.0130.21111390.18142668
2.013-2.05990.19781420.18682687
2.0599-2.11140.24191530.18682685
2.1114-2.16850.17161550.17712718
2.1685-2.23230.22081460.17452650
2.2323-2.30430.20611520.16792689
2.3043-2.38670.20491500.17032725
2.3867-2.48220.22461420.16772694
2.4822-2.59520.20751470.17172725
2.5952-2.7320.2081370.1652716
2.732-2.90320.19231470.16742754
2.9032-3.12730.18171320.17222743
3.1273-3.4420.18131360.1612787
3.442-3.93990.17561570.14772807
3.9399-4.96340.15561500.13132840
4.9634-54.3640.21061490.18913058
Refinement TLS params.

Method: refined / 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)
10.30890.16670.07180.22150.18930.57910.2427-0.1873-0.28270.47450.0954-0.04250.2519-0.20470.02230.3667-0.0378-0.0690.2480.04850.3574.98291.6149-15.7525
20.4437-0.25770.32370.4082-0.01451.1350.03360.0789-0.0996-0.0025-0.02780.01350.11750.0785-00.1550.01280.020.2157-0.00550.226610.417817.6769-26.0022
30.2477-0.141-0.24320.188-0.02911.22440.00640.0203-0.0339-0.0043-0.0395-0.0293-0.04010.0158-00.22210.0019-0.00060.20540.00290.19313.696329.4759-12.029
40.63290.06980.1360.37510.29170.4869-0.0224-0.0492-0.05640.08140.00890.0279-0.0311-0.101600.2180.0336-0.0070.17060.01110.2015-14.925136.6786-24.3409
50.13250.10840.02190.07710.03490.2109-0.09320.24890.0047-0.0729-0.00410.2158-0-0.136-0.0010.21730.0405-0.01950.2274-0.0140.255-15.322332.6482-43.1005
60.8673-0.1468-0.07060.3361-0.44651.02090.02750.1324-0.0772-0.1076-0.0360.04890.05-0.011800.19350.02230.00560.1868-0.0150.2047-0.67930.2831-40.4065
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 64 )A21 - 64
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 206 )A65 - 206
3X-RAY DIFFRACTION3chain 'A' and (resid 207 through 328 )A207 - 328
4X-RAY DIFFRACTION4chain 'A' and (resid 329 through 444 )A329 - 444
5X-RAY DIFFRACTION5chain 'A' and (resid 445 through 472 )A445 - 472
6X-RAY DIFFRACTION6chain 'A' and (resid 473 through 543 )A473 - 543

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