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- PDB-1mzy: Crystal Structure of Nitrite Reductase -

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Basic information

Entry
Database: PDB / ID: 1mzy
TitleCrystal Structure of Nitrite Reductase
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / Nitrite reductase / mutant M182T / gating mechanism / electron transfer
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, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like ...Nitrite reductase, copper-type / Multicopper oxidase, type 1 / 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
COPPER (II) ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsGuo, H. / Olesen, K. / Xue, Y. / Shapliegh, J. / Sjolin, L.
CitationJournal: To be Published
Title: The High resolution Crystal Structures of Nitrite Reductase and its mutant Met182Thr from Rhodobacter Sphaeroides Reveal a Gating Mechanism for the Electron Transfer to the Type 1 Copper Center
Authors: Guo, H. / Olesen, K. / Xue, Y. / Shapliegh, J. / Sjolin, L.
History
DepositionOct 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5416
Polymers36,3411
Non-polymers2005
Water5,693316
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)109,62318
Polymers109,0233
Non-polymers60015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area13720 Å2
ΔGint-130 kcal/mol
Surface area31340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.392, 71.392, 146.246
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe second and third parts of the biological assembly are generated by the three fold axis:

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Components

#1: Protein Copper-containing nitrite reductase / Nitrite Reductase / Cu-NIR


Mass: 36341.066 Da / Num. of mol.: 1 / Fragment: residues 41-371
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53239, EC: 1.7.99.3
#2: Chemical ChemComp-CU / COPPER (II) ION


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


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 1.97 Å3/Da / Density % sol: 37.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 6000 or 4000, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.018 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1999 / Details: mirror
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.018 Å / Relative weight: 1
ReflectionResolution: 1.46→17.54 Å / Num. all: 48257 / Num. obs: 48257 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 9.42 Å2 / Rmerge(I) obs: 0.204 / Rsym value: 0.184 / Net I/σ(I): 2.5
Reflection shellResolution: 1.46→1.54 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.8 / Num. unique all: 7003 / Rsym value: 0.365 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→17.54 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection
Rfree0.2099 1930
Rwork0.1846 -
all-48257
obs-48257
Refinement stepCycle: LAST / Resolution: 1.46→17.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2545 0 5 316 2866

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