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- PDB-1wa2: Crystal Structure Of H313Q Mutant Of Alcaligenes Xylosoxidans Nit... -

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Basic information

Entry
Database: PDB / ID: 1wa2
TitleCrystal Structure Of H313Q Mutant Of Alcaligenes Xylosoxidans Nitrite Reductase with nitrite bound
ComponentsDISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE,
KeywordsREDUCTASE / NITRITE REDUCTASE / H313Q MUTANT / NO2 / DENITRIFICATION
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 / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesALCALIGENES XYLOSOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsBarrett, M.L. / Harris, R.L. / Antonyuk, S.V. / Strange, R.W. / Hough, M.A. / Eady, R.R. / Sawers, G. / Hasnain, S.S.
CitationJournal: Biochemistry / Year: 2004
Title: Insights Into Redox Partner Interactions and Substrate Binding in Nitrite Reductase from Alcaligenes Xylosoxidans: Crystal Structures of the Trp138His and His313Gln Mutants
Authors: Barrett, M.L. / Harris, R.L. / Antonyuk, S.V. / Hough, M.A. / Ellis, M.J. / Sawers, G. / Eady, R.R. / Hasnain, S.S.
History
DepositionOct 22, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 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
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 / _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_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_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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE,
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1568
Polymers36,5611
Non-polymers5957
Water5,945330
1
X: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE,
hetero molecules

X: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE,
hetero molecules

X: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE,
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,46724
Polymers109,6823
Non-polymers1,78621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPQS
Unit cell
Length a, b, c (Å)89.641, 89.641, 143.569
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
11X-2012-

HOH

21X-2032-

HOH

31X-2048-

HOH

41X-2231-

HOH

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Components

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Protein , 1 types, 1 molecules X

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


Mass: 36560.512 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ALCALIGENES XYLOSOXIDANS (bacteria) / Variant: XYLOSOXIDANS / Plasmid: PENIRSP-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O68601

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Non-polymers , 6 types, 337 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE HIS 337 GLN, CHAIN X. (RESIDUE NUMBER 313 IN COORDINATE RECORDS BELOW).

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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: 3.05 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: CRYSTALS OF HIS313GLN NIR WERE GROWN BY THE HANGING-DROP VAPOUR DIFFUSION METHOD AT 21OC. 2ML OF 6-8 MG ML-1 PROTEIN IN 10 MM TRIS-HCL PH 7.1 WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR ...Details: CRYSTALS OF HIS313GLN NIR WERE GROWN BY THE HANGING-DROP VAPOUR DIFFUSION METHOD AT 21OC. 2ML OF 6-8 MG ML-1 PROTEIN IN 10 MM TRIS-HCL PH 7.1 WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION CONSISTING OF 25% PEG-MME 550, 10 MM ZINC SULPHATE, 0.1M MES PH 6.5 AND SUSPENDED OVER A 500 ML RESERVOIR. CRYSTALS OF BOTH MUTANTS WERE AN INTENSE BLUE COLOUR AND GREW WITHIN TWO DAYS TO APPROXIMATE DIMENSIONS 0.9 X 0.6 X 0.1 MM IN A RHOMBOHEDRAL MORPHOLOGY. FOR HIS313GLN_NO2.-, 10MM SODIUM NITRITE WAS ADDED TO THE RESERVOIR SOLUTION PRIOR TO CRYSTALLISATION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.48
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48 Å / Relative weight: 1
ReflectionResolution: 1.72→60 Å / Num. obs: 44676 / % possible obs: 97.5 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.7
Reflection shellResolution: 1.72→1.75 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OE1

1oe1


Resolution: 1.72→37.53 Å / Cor.coef. Fo:Fc: 0.957 / SU B: 1.867 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2257 5.1 %RANDOM
Rwork0.18 ---
obs0.182 44676 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20.28 Å20 Å2
2--0.57 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.72→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2523 0 24 330 2877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212626
X-RAY DIFFRACTIONr_bond_other_d0.0030.022337
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9483584
X-RAY DIFFRACTIONr_angle_other_deg0.94535441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1715333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022945
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02502
X-RAY DIFFRACTIONr_nbd_refined0.2340.2488
X-RAY DIFFRACTIONr_nbd_other0.2530.22731
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.21439
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2245
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.2139
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6531.51663
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.12822680
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7183963
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6764.5904
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: 1.72→1.76 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.274 182
Rwork0.246 3310

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