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- PDB-6qpz: Crystal structure of as isolated Y323E mutant of haem-Cu containi... -

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Basic information

Entry
Database: PDB / ID: 6qpz
TitleCrystal structure of as isolated Y323E mutant of haem-Cu containing nitrite reductase from Ralstonia pickettii
ComponentsCopper-containing nitrite reductase
KeywordsMETAL BINDING PROTEIN / haem and Cu containing nitrite reductase / inter-copper electron transfer
Function / homology
Function and homology information


nitrite reductase (NO-forming) / : / nitrite reductase (NO-forming) activity / electron transfer activity / periplasmic space / copper ion binding / heme binding
Similarity search - Function
Cytochrome C oxidase, cbb3-type, subunit III / Nitrite reductase, copper-type / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cytochrome c family profile. / Cytochrome c-like domain ...Cytochrome C oxidase, cbb3-type, subunit III / Nitrite reductase, copper-type / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cupredoxin / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / HEME C / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesRalstonia pickettii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsAntonyuk, S.V. / Shenoy, R.T. / Hedison, T.M. / Eady, R.R. / Hasnain, S.S. / Scrutton, N.S.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/N019380/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/N013972/1 United Kingdom
CitationJournal: Acs Catalysis / Year: 2019
Title: Unexpected Roles of a Tether Harboring a Tyrosine Gatekeeper Residue in Modular Nitrite Reductase Catalysis.
Authors: Hedison, T.M. / Shenoy, R.T. / Iorgu, A.I. / Heyes, D.J. / Fisher, K. / Wright, G.S.A. / Hay, S. / Eady, R.R. / Antonyuk, S.V. / Hasnain, S.S. / Scrutton, N.S.
History
DepositionFeb 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper-containing nitrite reductase
I: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4129
Polymers99,8292
Non-polymers1,5837
Water20,9871165
1
A: Copper-containing nitrite reductase
hetero molecules

A: Copper-containing nitrite reductase
hetero molecules

A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,98012
Polymers149,7433
Non-polymers2,2379
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area17940 Å2
ΔGint-209 kcal/mol
Surface area44170 Å2
MethodPISA
2
I: Copper-containing nitrite reductase
hetero molecules

I: Copper-containing nitrite reductase
hetero molecules

I: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,25615
Polymers149,7433
Non-polymers2,51312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area18730 Å2
ΔGint-211 kcal/mol
Surface area43800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.550, 127.550, 172.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1076-

HOH

21A-1146-

HOH

31A-1153-

HOH

41I-1073-

HOH

51I-1125-

HOH

61I-1151-

HOH

71I-1197-

HOH

81I-1198-

HOH

91I-1203-

HOH

101I-1209-

HOH

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Components

#1: Protein Copper-containing nitrite reductase


Mass: 49914.457 Da / Num. of mol.: 2 / Mutation: Y323E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia pickettii (bacteria) / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: I6NAW4, nitrite reductase (NO-forming)
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1165 / 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: 2.75 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES (pH7.5), 20% PEG 3350, 0.2 M Sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2018 / Details: mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.45→46.64 Å / Num. obs: 183931 / % possible obs: 98.5 % / Redundancy: 2.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.05 / Net I/σ(I): 8.8
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 2.5 % / Rmerge(I) obs: 1.167 / Mean I/σ(I) obs: 0.8 / CC1/2: 0.428 / Rpim(I) all: 0.905 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementResolution: 1.65→42.73 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 3.443 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.08 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17806 6234 5 %RANDOM
Rwork0.15838 ---
obs0.15937 118437 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.555 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20.42 Å20 Å2
2--0.83 Å20 Å2
3----2.7 Å2
Refinement stepCycle: 1 / Resolution: 1.65→42.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6859 0 96 1165 8120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0137371
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176776
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.66610084
X-RAY DIFFRACTIONr_angle_other_deg1.451.58415810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3025980
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14523.161348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.668151170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0921534
X-RAY DIFFRACTIONr_chiral_restr0.0770.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028453
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021491
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7731.1433714
X-RAY DIFFRACTIONr_mcbond_other0.7731.1423713
X-RAY DIFFRACTIONr_mcangle_it1.2831.7074657
X-RAY DIFFRACTIONr_mcangle_other1.2831.7094658
X-RAY DIFFRACTIONr_scbond_it1.2821.2843657
X-RAY DIFFRACTIONr_scbond_other1.2821.2853655
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0741.875391
X-RAY DIFFRACTIONr_long_range_B_refined5.85116.1368498
X-RAY DIFFRACTIONr_long_range_B_other5.49914.478146
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 462 -
Rwork0.371 8772 -
obs--99.34 %
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)
10.0923-0.0850.04890.1884-0.04060.0531-0.0157-0.0145-0.0413-0.0047-0.0260.01540.0028-0.02330.04160.01190.00190.02440.0241-0.0080.3282-10.726-15.957-0.435
20.23460.0307-0.06570.0403-0.01920.03280.00410.00120.04410.0068-0.02170.0207-0.01240.0060.01770.0156-0.0025-0.00160.0133-0.00490.203-8.498-56.367-27.932
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 600
2X-RAY DIFFRACTION2I4 - 600

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