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- PDB-1rzq: Crystal Structure of C-Terminal Despentapeptide Nitrite Reductase... -

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Basic information

Entry
Database: PDB / ID: 1rzq
TitleCrystal Structure of C-Terminal Despentapeptide Nitrite Reductase from Achromobacter Cycloclastes at pH5.0
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / denitrification / residue deletion / pH profile / Greek key beta barrel
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
ACETIC ACID / COPPER (II) ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesAchromobacter cycloclastes (bacteria)
MethodX-RAY DIFFRACTION / ISOMORPHOUS DIFFERENCE FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsLi, H.T. / Wang, C. / Chang, T. / Chang, W.C. / Liu, M.Y. / Le Gall, J. / Gui, L.L. / Zhang, J.P. / An, X.M. / Chang, W.R.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: pH-profile crystal structure studies of C-terminal despentapeptide nitrite reductase from Achromobacter cycloclastes
Authors: Li, H.T. / Wang, C. / Chang, T. / Chang, W.C. / Liu, M.Y. / Le Gall, J. / Gui, L.L. / Zhang, J.P. / An, X.M. / Chang, W.R.
History
DepositionDec 26, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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.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_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: Copper-containing nitrite reductase
B: Copper-containing nitrite reductase
C: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,73418
Polymers109,6323
Non-polymers1,10215
Water14,340796
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12180 Å2
ΔGint-149 kcal/mol
Surface area33540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.020, 117.440, 122.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a trimer in the asymmetric unit

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Components

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


Mass: 36544.160 Da / Num. of mol.: 3 / Fragment: C-Terminal Despentapeptide Nitrite Reductase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter cycloclastes (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): M15(PREP4) / References: UniProt: P25006, nitrite reductase (NO-forming)
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 796 / 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: 3 Å3/Da / Density % sol: 58.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.4M ammonium sulfate, 0.1M acetate acid pH 5.0, 0.2M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: CONVENTIONAL Cu / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 73244 / Num. obs: 73098 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.4
Reflection shellResolution: 2.2→2.25 Å / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 3 / % possible all: 99.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
CNSphasing
RefinementMethod to determine structure: ISOMORPHOUS DIFFERENCE FOURIER SYNTHESIS
Starting model: PDB ENTRY 1RZP

1rzp


Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2489 3.4 %RANDOM
Rwork0.181 ---
all-73180 --
obs-69668 95.2 %-
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1--2.306 Å20 Å20 Å2
2--4.192 Å20 Å2
3----1.885 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7644 0 31 812 8487
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0052
X-RAY DIFFRACTIONc_angle_deg1.57
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2.2→2.28 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.259 244 3.38 %
Rwork0.231 6210 -
obs--89.5 %

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