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- PDB-6rtd: Dihydro-heme d1 dehydrogenase NirN in complex with DHE -

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Basic information

Entry
Database: PDB / ID: 6rtd
TitleDihydro-heme d1 dehydrogenase NirN in complex with DHE
ComponentsCytochrome c
KeywordsOXIDOREDUCTASE / 8-bladed beta-propeller heme d1 biosynthesis dehydrogenase
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors / nitrite reductase (NO-forming) / heme biosynthetic process / periplasmic space / electron transfer activity / oxidoreductase 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 D / HEME C / Cytochrome c / Dihydro-heme d1 dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.36 Å
AuthorsKluenemann, T. / Preuss, A. / Layer, G. / Blankenfeldt, W.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationGRK 2223 Germany
German Research FoundationLA 2412 Germany
Citation
Journal: J.Mol.Biol. / Year: 2019
Title: Crystal Structure of Dihydro-Heme d1Dehydrogenase NirN from Pseudomonas aeruginosa Reveals Amino Acid Residues Essential for Catalysis.
Authors: Klunemann, T. / Preuss, A. / Adamczack, J. / Rosa, L.F.M. / Harnisch, F. / Layer, G. / Blankenfeldt, W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Data processing and analysis with the autoPROC toolbox.
Authors: Vonrhein, C. / Flensburg, C. / Keller, P. / Sharff, A. / Smart, O. / Paciorek, W. / Womack, T. / Bricogne, G.
History
DepositionMay 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_chiral / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,4937
Polymers111,7402
Non-polymers2,7525
Water5,765320
1
A: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2914
Polymers55,8701
Non-polymers1,4213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2013
Polymers55,8701
Non-polymers1,3312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)191.382, 54.590, 132.135
Angle α, β, γ (deg.)90.000, 131.935, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Cytochrome c / Nitrite reductase


Mass: 55870.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: nirS_1, EFK27_00335, EGV95_02815, IPC669_26980, PAERUG_E15_London_28_01_14_07983, RW109_RW109_01113
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0C7D2F2, UniProt: Q9I609*PLUS, nitrite reductase (NO-forming)
#2: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical ChemComp-DHE / HEME D


Mass: 712.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O10
#4: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
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: 46.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 13.2%(w/v) PEG3350, 4.33% (w/v) PGA200-400 0.1 M Tris/HCl pH 7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.36→45.09 Å / Num. obs: 42328 / % possible obs: 99.91 % / Redundancy: 6.8 % / Biso Wilson estimate: 38.92 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.053 / Net I/σ(I): 10.6
Reflection shellResolution: 2.36→2.44 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4185 / CC1/2: 0.824 / Rpim(I) all: 0.354 / % possible all: 99.93

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIXdev_3112refinement
autoPROCdata collection
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.36→45.09 Å / SU ML: 0.2819 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.9406
RfactorNum. reflection% reflection
Rfree0.235 2152 5.08 %
Rwork0.1915 --
obs0.1938 42338 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 59.91 Å2
Refinement stepCycle: LAST / Resolution: 2.36→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7153 0 190 320 7663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00227752
X-RAY DIFFRACTIONf_angle_d0.582310658
X-RAY DIFFRACTIONf_chiral_restr0.04481116
X-RAY DIFFRACTIONf_plane_restr0.00441392
X-RAY DIFFRACTIONf_dihedral_angle_d11.78384529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.410.31821440.26082663X-RAY DIFFRACTION99.89
2.41-2.470.25941560.2552636X-RAY DIFFRACTION99.86
2.47-2.540.30581360.25082636X-RAY DIFFRACTION99.96
2.54-2.610.28351310.24712699X-RAY DIFFRACTION100
2.61-2.70.2711550.23432632X-RAY DIFFRACTION99.86
2.7-2.80.29221390.23192645X-RAY DIFFRACTION99.96
2.8-2.910.27281460.22232693X-RAY DIFFRACTION100
2.91-3.040.25521370.22272673X-RAY DIFFRACTION99.96
3.04-3.20.26071560.22342661X-RAY DIFFRACTION99.89
3.2-3.40.251250.21022693X-RAY DIFFRACTION99.93
3.4-3.660.26141260.18332703X-RAY DIFFRACTION99.96
3.66-4.030.21371160.17772671X-RAY DIFFRACTION99.96
4.03-4.610.20261780.14972676X-RAY DIFFRACTION99.83
4.61-5.810.20731500.1452707X-RAY DIFFRACTION99.93
5.81-45.090.18331570.17242798X-RAY DIFFRACTION99.83
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)
13.85593395561-0.1746551539490.5616914398763.09171219355-2.635210746436.607690475840.469079489604-0.400926162194-0.624943550586-0.0140898367254-0.1351710932640.07857309649950.876923889260.559345086141-0.3058372309840.5235857813020.161907183053-0.1008640312020.440436205147-0.01058101382310.43880102475853.6885898631-9.5497929348184.3264192422
22.417662937970.3620101353330.4642443256141.68093608029-0.1485538219412.302159266050.0580362688377-0.307619835141-0.09522970496720.08052965819890.0725965069760.04411602627210.230148906087-0.273039437157-0.0922941427550.2511279669370.02002651650930.01409473725660.2620432881430.04933651958480.24008846373134.19087837163.9570620292570.528783959
34.458114203821.17344681517-2.952456755727.479614607241.63123051432.87970133009-0.128586279998-0.7995083689540.7219292661310.8732582478220.32245397325-0.529014808324-0.9375336935090.0340574694402-0.1206891755460.6273649992850.0430650011166-0.05674099171060.63744980017-0.1108466219830.58055008792934.639289930623.368940803782.8308859495
42.510887398460.613944222614-0.4160330181732.712018286310.5119460865073.387856591690.213403472932-0.7449900737460.09083236316380.601530685729-0.1726505327680.144539087139-0.197558546629-0.633059389242-0.04080727227830.509006237649-0.02100235464780.07778560237190.9030319967060.06794296921640.36637929292424.840394967110.187718616992.4868970613
55.370527305970.80850449988-0.5190936826966.17877997847-1.092051846952.668278202920.267645601540.3704585497640.05571104349670.26675568976-0.376102017637-0.385092786591-0.7587268158140.6674836961370.07239831659580.510853476718-0.175135940636-0.05139530757050.5591249580830.1334104124030.33075066818533.137127906918.780814219.8374817266
61.059363997030.143665766557-0.1892182169230.763983636160.3288764152281.78143991205-0.0423230303460.153932954870.0930454940845-0.09286511164760.03991542812580.116847989098-0.1652946251160.00702153535276-0.01061235632210.21634898205-0.0352924891496-0.02374506653480.217688281080.06274156195320.32509752893426.60292328717.9643096651238.0636440296
72.592614169830.225653308989-1.861889308155.943921378621.277914357151.92583555546-0.1570167487140.957477218248-0.466200408623-0.41996966594-0.0535007014873-0.1230754070230.600381265803-0.1078781402090.0312250499850.526900189899-0.0803514674732-0.05818126853860.550148814848-0.03568985048240.47570246514118.7404685078-13.149044358531.0925262141
83.114039154770.04351957204690.3993867771383.423803318460.707890378392.69121609456-0.208705131920.570858510856-0.0363389378677-0.56749801059-0.1512470461670.386543604485-0.0564773124183-0.2145015137340.3263226068710.313989253299-0.0735734185252-0.09249072952810.5475824956640.06091629799940.4788070329984.79408663493-0.34644551822729.1346745002
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 85 )
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 281 )
3X-RAY DIFFRACTION3chain 'A' and (resid 282 through 334 )
4X-RAY DIFFRACTION4chain 'A' and (resid 335 through 468 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 48 )
6X-RAY DIFFRACTION6chain 'B' and (resid 49 through 281 )
7X-RAY DIFFRACTION7chain 'B' and (resid 282 through 332 )
8X-RAY DIFFRACTION8chain 'B' and (resid 333 through 468 )

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