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- PDB-2xxg: STRUCTURE OF THE N90S MUTANT OF NITRITE REDUCTASE FROM ALCALIGENE... -

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Basic information

Entry
Database: PDB / ID: 2xxg
TitleSTRUCTURE OF THE N90S MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
ComponentsDISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
KeywordsOXIDOREDUCTASE
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 / DI(HYDROXYETHYL)ETHER / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesACHROMOBACTER XYLOSOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHough, M.A. / Eady, R.R. / Hasnain, S.S.
Citation
Journal: Biochemistry / Year: 2008
Title: Identification of the Proton Channel to the Active Site Type 2 Cu Centre of Nitrite Reductase: Structural and Enzymatic Properties of the His254Phe and Asn90Ser Mutants
Authors: Hough, M.A. / Eady, R.R. / Hasnain, S.S.
#1: Journal: Biochemistry / Year: 2011
Title: Proton-Coupled Electron Transfer in the Catalytic Cycle of Alcaligenes Xylosoxidans Copper-Dependent Nitrite Reductase.
Authors: Leferink, N.G.H. / Han, C. / Antonyuk, S.V. / Heyes, D.J. / Rigby, S.E.J. / Hough, M.A. / Eady, R.R. / Scrutton, N.S. / Hasnain, S.S.
History
DepositionNov 10, 2010Deposition site: PDBE / Processing site: PDBE
SupersessionMay 18, 2011ID: 2JL0
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 11, 2020Group: Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_status / pdbx_struct_special_symmetry
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf
Revision 2.1Dec 20, 2023Group: 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 / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _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
C: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,16320
Polymers73,0532
Non-polymers2,11018
Water11,692649
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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)112,74430
Polymers109,5793
Non-polymers3,16527
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 area19510 Å2
ΔGint-185.5 kcal/mol
Surface area34680 Å2
MethodPISA
2
C: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
hetero molecules

C: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
hetero molecules

C: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,74430
Polymers109,5793
Non-polymers3,16527
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+y+1,-x-1,z1
crystal symmetry operation2_435-y-1,x-y-2,z1
Buried area18910 Å2
ΔGint-188 kcal/mol
Surface area33420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.552, 89.552, 287.678
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-2029-

HOH

21A-2040-

HOH

31A-2045-

HOH

41A-2129-

HOH

51A-2327-

HOH

61C-2041-

HOH

71C-2070-

HOH

81C-2251-

HOH

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE / NITRITE REDUCTASE / NIR


Mass: 36526.473 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACHROMOBACTER XYLOSOXIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O68601

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Non-polymers , 6 types, 667 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-CU / COPPER (II) ION / Copper


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


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 649 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 114 TO SER ENGINEERED RESIDUE IN CHAIN C, ASN 114 TO SER
Nonpolymer detailsPYROGLUTAMIC ACID (PCA): MODIFIED N-TERMINAL RESIDUE

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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: 3.04 Å3/Da / Density % sol: 59.52 % / Description: NONE
Crystal growpH: 6.5 / Details: PEG 550 MME, ZNSO4, MES PH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→29.1 Å / Num. obs: 106504 / % possible obs: 93.8 % / Observed criterion σ(I): -10 / Redundancy: 2.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.1 / % possible all: 60.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OE1

1oe1


Resolution: 1.6→29.16 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.21074 5333 5 %RANDOM
Rwork0.1675 ---
obs0.1696 101170 93.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.175 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.1 Å20 Å2
2--0.2 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5084 0 110 649 5843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225392
X-RAY DIFFRACTIONr_bond_other_d00.023633
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.9677345
X-RAY DIFFRACTIONr_angle_other_deg4.21938893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3215687
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8624.389221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33615817
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8841520
X-RAY DIFFRACTIONr_chiral_restr0.2130.2801
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216005
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021017
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_it1.4141.53361
X-RAY DIFFRACTIONr_mcbond_other5.4671.51373
X-RAY DIFFRACTIONr_mcangle_it2.10925431
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.27232031
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6554.51906
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.86439025
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.599→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 225 -
Rwork0.322 4627 -
obs--58.24 %

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