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- PDB-2bw4: Atomic Resolution Structure of Resting State of the Achromobacter... -

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Basic information

Entry
Database: PDB / ID: 2bw4
TitleAtomic Resolution Structure of Resting State of the Achromobacter cycloclastes Cu Nitrite Reductase
ComponentsCOPPER-CONTAINING NITRITE REDUCTASE
KeywordsOXIDOREDUCTASE / DENITRIFICATION / CATALYSIS / ENZYME MECHANISM / NITRATE ASSIMILATION
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, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin ...Nitrite reductase, copper-type / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / COPPER (II) ION / MALONATE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesACHROMOBACTER CYCLOCLASTES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsAntonyuk, S.V. / Strange, R.W. / Sawers, G. / Eady, R.R. / Hasnain, S.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Atomic Resolution Structures of Resting-State, Substrate- and Product-Complexed Cu-Nitrite Reductase Provide Insight Into Catalytic Mechanism
Authors: Antonyuk, S.V. / Strange, R.W. / Sawers, G. / Eady, R.R. / Hasnain, S.S.
History
DepositionJul 12, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_validate_polymer_linkage / 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 / _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.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 / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_1 / _pdbx_validate_polymer_linkage.label_alt_id_2 / _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
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
A: COPPER-CONTAINING NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,71710
Polymers37,0601
Non-polymers6579
Water11,403633
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)113,15230
Polymers111,1793
Non-polymers1,97227
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-y+1,z+1/2,-x+1/21
crystal symmetry operation7_564-z+1/2,-x+1,y-1/21
MethodPQS
Unit cell
Length a, b, c (Å)95.414, 95.414, 95.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-2025-

HOH

21A-2026-

HOH

31A-2055-

HOH

41A-2058-

HOH

51A-2092-

HOH

61A-2231-

HOH

71A-2232-

HOH

81A-2273-

HOH

91A-2503-

HOH

101A-2612-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 37059.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ACHROMOBACTER CYCLOCLASTES (bacteria) / References: UniProt: P25006, nitrite reductase (NO-forming)

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Non-polymers , 5 types, 642 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-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 633 / 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 Å3/Da / Density % sol: 36.6 %
Crystal growpH: 5
Details: 1.6M AMMONIUM SULPHATE, 100MM SODIUM ACETATE, PH 4.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.074
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 30, 2005 / Details: MIRRORS
RadiationMonochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.074 Å / Relative weight: 1
ReflectionResolution: 0.9→19.5 Å / Num. obs: 208276 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 5.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 24
Reflection shellResolution: 0.9→0.92 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2 / % possible all: 85.9

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NIF

1nif


Resolution: 0.9→19.48 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.403 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.134 8169 4 %RANDOM
Rwork0.117 ---
obs0.118 195768 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 7 Å2
Refinement stepCycle: LAST / Resolution: 0.9→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 35 633 3249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223014
X-RAY DIFFRACTIONr_bond_other_d0.0020.022701
X-RAY DIFFRACTIONr_angle_refined_deg2.1671.9434145
X-RAY DIFFRACTIONr_angle_other_deg2.33236341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9165398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.515494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0671516
X-RAY DIFFRACTIONr_chiral_restr0.1350.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023435
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02599
X-RAY DIFFRACTIONr_nbd_refined0.2860.2554
X-RAY DIFFRACTIONr_nbd_other0.2170.22606
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1030.21531
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2970.2431
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3550.249
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.2171
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2630.2107
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8191.52375
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.21323010
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.02531373
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6974.51112
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: 0.9→0.92 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.365 521
Rwork0.332 13102

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