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- PDB-8qgf: CRYSTAL STRUCTURE OF AS-ISOLATED M148L MUTANT OF THREE-DOMAIN HEM... -

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Basic information

Entry
Database: PDB / ID: 8qgf
TitleCRYSTAL STRUCTURE OF AS-ISOLATED M148L MUTANT OF THREE-DOMAIN HEME-CU NITRITE REDUCTASE FROM RALSTONIA PICKETTII
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / HAEM AND CU CONTAINING NITRITE REDUCTASE / ELECTRON TRANSFER / REDOX REACTIONS / METAL BINDING PROTEIN
Function / homology
Function and homology information


nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / periplasmic space / electron transfer activity / copper ion binding / heme binding
Similarity search - Function
: / Nitrite reductase, copper-type / Cytochrome c / Multicopper oxidase, N-terminal / Multicopper oxidase / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / HEME C / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesRalstonia pickettii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.32 Å
AuthorsPetchyam, N. / Antonyuk, S. / Hasnain, S.S.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)BB/N013972/1 United Kingdom
UK Research and Innovation (UKRI)BB/L006960/1 United Kingdom
CitationJournal: To Be Published
Title: Structural studies of haem three-domain copper nitrite reductase mutants from Ralstonia pickettii
Authors: Petchyam, N. / Antonyuk, S. / Hasnain, S.S.
History
DepositionSep 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 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: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3444
Polymers48,5981
Non-polymers7463
Water13,259736
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)148,03112
Polymers145,7943
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 area18060 Å2
ΔGint-209 kcal/mol
Surface area43850 Å2
Unit cell
Length a, b, c (Å)127.952, 127.952, 86.249
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-1242-

HOH

21A-1262-

HOH

31A-1277-

HOH

41A-1304-

HOH

51A-1307-

HOH

61A-1319-

HOH

71A-1335-

HOH

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Components

#1: Protein Copper-containing nitrite reductase


Mass: 48597.957 Da / Num. of mol.: 1 / Mutation: M148L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia pickettii (bacteria) / Plasmid: pET26b-M148L_RpNiR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6NAW4
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 736 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-tris propane pH 6.3, 0.1 M sodium citrate, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.32→46.66 Å / Num. obs: 124091 / % possible obs: 99.4 % / Redundancy: 5.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.067 / Rrim(I) all: 0.152 / Χ2: 0.98 / Net I/av σ(I): 6.4 / Net I/σ(I): 6.4
Reflection shellResolution: 1.32→1.34 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.888 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 5450 / CC1/2: 0.265 / Rpim(I) all: 0.961 / Rrim(I) all: 2.124 / Χ2: 0.97 / % possible all: 87.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
xia2data reduction
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.32→46.66 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 2.199 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16176 5839 4.7 %RANDOM
Rwork0.13401 ---
obs0.1353 118239 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20.5 Å2-0 Å2
2--0.99 Å2-0 Å2
3----3.22 Å2
Refinement stepCycle: 1 / Resolution: 1.32→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3423 0 45 736 4204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133944
X-RAY DIFFRACTIONr_bond_other_d0.0080.0153732
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.6695439
X-RAY DIFFRACTIONr_angle_other_deg1.431.598679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0545552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94123.196194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64415649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3421519
X-RAY DIFFRACTIONr_chiral_restr0.1030.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024671
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02905
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_it1.1261.5341945
X-RAY DIFFRACTIONr_mcbond_other1.1041.5321944
X-RAY DIFFRACTIONr_mcangle_it1.412.3112460
X-RAY DIFFRACTIONr_mcangle_other1.412.3132461
X-RAY DIFFRACTIONr_scbond_it1.5911.71998
X-RAY DIFFRACTIONr_scbond_other1.5921.71996
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7382.4872931
X-RAY DIFFRACTIONr_long_range_B_refined3.27220.9034675
X-RAY DIFFRACTIONr_long_range_B_other2.49419.1324415
X-RAY DIFFRACTIONr_rigid_bond_restr3.24537675
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.32→1.35 Å
RfactorNum. reflection% reflection
Rfree0.356 416 -
Rwork0.338 8086 -
obs--92.06 %

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