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- PDB-4paz: OXIDIZED MUTANT P80A PSEUDOAZURIN FROM A. FAECALIS -

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Basic information

Entry
Database: PDB / ID: 4paz
TitleOXIDIZED MUTANT P80A PSEUDOAZURIN FROM A. FAECALIS
ComponentsPSEUDOAZURIN
KeywordsELECTRON TRANSFER / CUPROPROTEIN
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Pseudoazurin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like ...Pseudoazurin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Pseudoazurin
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.76 Å
AuthorsAdman, E.T. / Libeu, C.A.P.
Citation
Journal: Biochemistry / Year: 1997
Title: Site-directed mutants of pseudoazurin: explanation of increased redox potentials from X-ray structures and from calculation of redox potential differences.
Authors: Libeu, C.A. / Kukimoto, M. / Nishiyama, M. / Horinouchi, S. / Adman, E.T.
#1: Journal: Protein Eng. / Year: 1992
Title: Site-Directed Mutagenesis of Pseudoazurin from Alcaligenes Faecalis S-6; Pro80Ala Mutant Exhibits Marked Increase in Reduction Potential
Authors: Nishiyama, M. / Suzuki, J. / Ohnuki, T. / Chang, H.C. / Horinouchi, S. / Turley, S. / Adman, E.T. / Beppu, T.
#2: Journal: J.Biol.Chem. / Year: 1989
Title: A 2.0-A Structure of the Blue Copper Protein (Cupredoxin) from Alcaligenes Faecalis S-6
Authors: Adman, E.T. / Turley, S. / Bramson, R. / Petratos, K. / Banner, D. / Tsernoglou, D. / Beppu, T. / Watanabe, H.
History
DepositionFeb 20, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PSEUDOAZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4212
Polymers13,3571
Non-polymers641
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.060, 50.060, 98.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein PSEUDOAZURIN


Mass: 13357.474 Da / Num. of mol.: 1 / Mutation: P80A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Strain: S-6 / Cellular location: PERIPLASM / Gene: POTENTIAL / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P04377
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.96 %
Crystal growpH: 7
Details: 50MM SODIUM PHOSPHATE WITH 75% SATURATED AMMONIUM SULFATE, pH 7.0
Crystal grow
*PLUS
pH: 6.8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein11
220 mMphosphate11
342 %satammonium sulfate11

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Dec 1, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.76→26.2 Å / Num. obs: 12172 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 23.9
Reflection shellResolution: 1.76→1.8 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 7.6
Reflection
*PLUS
% possible obs: 86 %
Reflection shell
*PLUS
% possible obs: 55 %

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Processing

Software
NameClassification
SHELXLrefinement
XENGENdata reduction
XENGENdata scaling
RefinementResolution: 1.76→26.2 Å / Num. parameters: 4045 / Num. restraintsaints: 3788 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: COPPER-LIGAND DISTANCES NOT RESTRAINED; CU + S REFINED ANISOTROPICALLY
RfactorNum. reflection
all0.164 11974
obs0.164 -
Solvent computationSolvent model: BABINET'S PRINCIPLE (SHELX-93)
Refine analyzeNum. disordered residues: 0
Refinement stepCycle: LAST / Resolution: 1.76→26.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 1 71 1002
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.16
X-RAY DIFFRACTIONs_zero_chiral_vol0.084
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.114
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.019
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.038
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.167 / Rfactor obs: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_angle_d / Dev ideal: 0.019

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