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- PDB-4csz: STRUCTURE OF F306C MUTANT OF NITRITE REDUCTASE FROM Achromobacter... -

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Basic information

Entry
Database: PDB / ID: 4csz
TitleSTRUCTURE OF F306C MUTANT OF NITRITE REDUCTASE FROM Achromobacter XYLOSOXIDANS WITH NITRITE BOUND
ComponentsDISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
KeywordsOXIDOREDUCTASE / ELECTRON TRANSFER / MICROBIAL ATP-GENERATING RESPIRATORY DENTRIFICATION PATHWAY
Function / homology
Function and homology information


denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / periplasmic space / copper ion binding
Similarity search - Function
Nitrite reductase, copper-type / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / NITRITE ION / DI(HYDROXYETHYL)ETHER / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesACHROMOBACTER XYLOSOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLeferink, N.G.H. / Antonyuk, S.V. / Houwman, J.A. / Scrutton, N.S. / REady, R. / Hasnain, S.S.
CitationJournal: Nat.Commun. / Year: 2014
Title: Impact of Residues Remote from the Catalytic Centre on Enzyme Catalysis of Copper Nitrite Reductase.
Authors: Leferink, N.G.H. / Antonyuk, S.V. / Houwman, J.A. / Scrutton, N.S. / Eady, R.R. / Hasnain, S.S.
History
DepositionMar 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,13512
Polymers36,3981
Non-polymers73711
Water5,549308
1
A: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
hetero molecules

A: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
hetero molecules

A: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,40636
Polymers109,1953
Non-polymers2,21133
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area17340 Å2
ΔGint-715 kcal/mol
Surface area33290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.570, 89.570, 144.011
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-2076-

HOH

21A-2125-

HOH

31A-2262-

HOH

41A-2272-

HOH

51A-2313-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE


Mass: 36398.367 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACHROMOBACTER XYLOSOXIDANS (bacteria) / Strain: IW2 IWASAKI / Plasmid: PET26 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O68601, nitrite reductase (NO-forming)

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Non-polymers , 5 types, 319 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsMUTATION F306C

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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: 3.1 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 6.5
Details: 15% PEG550 MME, 50 MM ZNSO4, AND 50 MM MES BUFFER, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2012 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→52.77 Å / Num. obs: 43456 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CSP

2csp


Resolution: 1.75→68.29 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.573 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20993 2185 5 %RANDOM
Rwork0.17821 ---
obs0.17983 41268 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.367 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.22 Å20 Å2
2--0.44 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 1.75→68.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2562 0 19 308 2889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192712
X-RAY DIFFRACTIONr_bond_other_d0.0020.022605
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.9613697
X-RAY DIFFRACTIONr_angle_other_deg0.78636029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1475352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74924.071113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61915446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3521513
X-RAY DIFFRACTIONr_chiral_restr0.0890.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213078
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02601
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_it1.8752.751357
X-RAY DIFFRACTIONr_mcbond_other1.8742.7461356
X-RAY DIFFRACTIONr_mcangle_it2.754.1141699
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9922.9371355
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 182 -
Rwork0.302 3021 -
obs--99.94 %

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