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

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Basic information

Entry
Database: PDB / ID: 6rte
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 / heme biosynthetic process / 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 / C-type cytochrome / Dihydro-heme d1 dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: 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 1.2Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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_label_asym_id / _struct_conn.ptnr2_label_atom_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)113,0685
Polymers111,7402
Non-polymers1,3273
Water13,259736
1
A: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5793
Polymers55,8701
Non-polymers7092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4892
Polymers55,8701
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)191.123, 54.957, 131.896
Angle α, β, γ (deg.)90.000, 132.417, 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-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 736 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 11.25%(w/v) PEG8000 5.22%(w/v) PGA 200-400 0.1M Tris/HCl pH 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.94→51.21 Å / Num. obs: 75298 / % possible obs: 99.92 % / Redundancy: 10.6 % / Biso Wilson estimate: 28.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.051 / Net I/σ(I): 11.1
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 10.7 % / Rmerge(I) obs: 2.117 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7445 / CC1/2: 0.563 / Rpim(I) all: 0.667 / % possible all: 99.93

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Processing

Software
NameVersionClassification
autoPROCdev_3112data collection
PHENIXdev_3112refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NIR

1nir


Resolution: 1.94→51.21 Å / SU ML: 0.1819 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.4097
RfactorNum. reflection% reflection
Rfree0.1978 3775 5.01 %
Rwork0.1674 --
obs0.169 75285 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.63 Å2
Refinement stepCycle: LAST / Resolution: 1.94→51.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7165 0 92 736 7993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00567524
X-RAY DIFFRACTIONf_angle_d0.772810308
X-RAY DIFFRACTIONf_chiral_restr0.0521093
X-RAY DIFFRACTIONf_plane_restr0.00561355
X-RAY DIFFRACTIONf_dihedral_angle_d13.00674438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.960.27031240.26362666X-RAY DIFFRACTION99.96
1.96-1.990.29391400.24712609X-RAY DIFFRACTION99.96
1.99-2.020.30521250.24372641X-RAY DIFFRACTION99.96
2.02-2.050.2351160.22752647X-RAY DIFFRACTION100
2.05-2.080.27011090.232641X-RAY DIFFRACTION100
2.08-2.110.23231270.22382680X-RAY DIFFRACTION99.96
2.11-2.140.27291360.21042577X-RAY DIFFRACTION100
2.14-2.180.24321620.20092622X-RAY DIFFRACTION100
2.18-2.220.23091490.19712629X-RAY DIFFRACTION100
2.22-2.260.23711340.18842663X-RAY DIFFRACTION100
2.26-2.310.21141330.17792655X-RAY DIFFRACTION99.89
2.31-2.360.20411310.17242618X-RAY DIFFRACTION99.89
2.36-2.410.17041750.17032619X-RAY DIFFRACTION99.96
2.41-2.480.20731570.16132608X-RAY DIFFRACTION99.96
2.48-2.540.23551540.16772603X-RAY DIFFRACTION99.96
2.54-2.620.19011570.16562661X-RAY DIFFRACTION100
2.62-2.70.22691450.16762604X-RAY DIFFRACTION100
2.7-2.80.221570.17262628X-RAY DIFFRACTION100
2.8-2.910.2371960.17042709X-RAY DIFFRACTION100
2.91-3.040.1951450.16922628X-RAY DIFFRACTION100
3.04-3.20.19271400.1692665X-RAY DIFFRACTION100
3.2-3.40.19631410.16352647X-RAY DIFFRACTION100
3.4-3.670.18441590.15642652X-RAY DIFFRACTION100
3.67-4.040.17821500.14342647X-RAY DIFFRACTION100
4.04-4.620.1461300.12772701X-RAY DIFFRACTION100
4.62-5.820.14711410.13352703X-RAY DIFFRACTION100
5.82-51.210.2051420.17522787X-RAY DIFFRACTION99.9
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)
13.120760983280.05321280585530.6961407622262.53762007291-0.5913124059183.533645741760.499069039153-0.304640328624-0.649256376397-0.0174238585801-0.1045169340240.2084272617430.4841928108030.192212400327-0.3847690071240.4074602177010.056855458268-0.06938137290240.4048123581650.07884721168150.35367929056351.3380226854-10.188359461586.6007965661
21.81497763694-0.2257819066290.4296175540720.8561969772670.08251490574461.386833664430.0577689310567-0.240344694362-0.1244745502960.03333141509641.04559201781E-50.04082800118860.0666993443391-0.130167971553-0.04599141998310.186818495229-0.01545689662070.005844977160350.1847743955710.02645387434330.15841353748134.85230980243.2275544893769.5482682393
33.793137677240.393741643790.04206130105772.307517284670.7195205455641.91415469968-0.208852853992-0.9358236678220.6078260687230.526260319315-0.185849502295-0.407437581673-0.8627258648220.1821345130330.4470128225780.637716976512-0.0858684473777-0.07392803244090.515460840233-0.05571864758510.48678436410737.339627992224.327219733579.8185216957
41.834784356650.555326094677-0.06174333305051.75104810635-0.02415234899811.732284713620.289743737861-0.6953280884740.1145015734080.671862533369-0.2065633575810.0360967009337-0.415303668804-0.0882957366708-0.0850457431090.639992538969-0.08258576373540.05953479419130.7264203236080.004911575710640.30932600973423.448558049611.621136730291.0847977286
51.23301010260.00737120626567-0.4484697813640.5853633365560.02968597395081.44188956860.01541629054750.178650350902-0.0117773935508-0.06841965986970.004032607550850.0123302416709-0.0110344566617-0.0118718055646-0.02436783463360.180231631521-0.0138832162561-0.014388487670.1744244137610.005397108863320.2194319796426.53579816487.4154984191835.1816311178
62.084330002450.1672755546580.452752310692.742498091260.1804444321382.40389429983-0.05571037737980.363902134479-0.148584182098-0.3181302548660.0103905821053-0.002821983267910.1711375713150.03867862536210.04877397896410.208281236433-0.03085696100080.003900941401260.270555894338-0.00729306874750.2489983667526.46099575514-3.3015396422729.2255880346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 75 )
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 274 )
3X-RAY DIFFRACTION3chain 'A' and (resid 275 through 328 )
4X-RAY DIFFRACTION4chain 'A' and (resid 329 through 480 )
5X-RAY DIFFRACTION5chain 'B' and (resid 15 through 302 )
6X-RAY DIFFRACTION6chain 'B' and (resid 303 through 480 )

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