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- PDB-1pzc: APO-PSEUDOAZURIN (METAL FREE PROTEIN) -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1pzc
TitleAPO-PSEUDOAZURIN (METAL FREE PROTEIN)
ComponentsPSEUDOAZURIN
KeywordsELECTRON TRANSFER (CUPROPROTEIN) / APOPROTEIN / METAL FREE PROTEIN
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
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsPetratos, K.
Citation
Journal: Febs Lett. / Year: 1995
Title: The crystal structure of apo-pseudoazurin from Alcaligenes faecalis S-6.
Authors: Petratos, K. / Papadovasilaki, M. / Dauter, Z.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Refinement of the Structure of Pseudoazurin from Alcaligenes Faecalis S-6 at 1.55 Angstroms Resolution
Authors: Petratos, K. / Dauter, Z. / Wilson, K.S.
History
DepositionFeb 22, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PSEUDOAZURIN


Theoretical massNumber of molelcules
Total (without water)13,3841
Polymers13,3841
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.500, 49.500, 99.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Atom site foot note1: CIS PROLINE - PRO 20 / 2: ATOM O HOH 136 WAS REFINED WITH OCCUPANCY SET TO 0.50. / 3: ATOM O HOH 137 WAS REFINED WITH OCCUPANCY SET TO 0.50.

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Components

#1: Protein PSEUDOAZURIN


Mass: 13383.511 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: APO FORM / Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Strain: S-6 / Plasmid: PUB1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P04377
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Compound detailsDE-METALLIZED CUPROPROTEIN WITH 100 MM KCN AT PH 6.7.
Source detailsMOLECULE_NAME: PSEUDOAZURIN. THE PSEUDOAZURIN GENE FROM A. FAECALIS (438 B.P.) WAS EXPRESSED UNDER ...MOLECULE_NAME: PSEUDOAZURIN. THE PSEUDOAZURIN GENE FROM A. FAECALIS (438 B.P.) WAS EXPRESSED UNDER THE CONTROL OF BOTH LAC AND TAC PROMOTERS.

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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: 2.61 Å3/Da / Density % sol: 52.95 %
Crystal growpH: 6.7 / Details: pH 6.7
Crystal grow
*PLUS
pH: 5.7 / Method: vapor diffusion / Details: Petratos, K., (1987) FEBS Lett., 218, 209.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.5 %protein 1drop
250 mM1dropCH3COONH4
31.5 Mammonium sulfate1drop
43.0 Mammonium sulfate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.87 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 13, 1994
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionNum. obs: 11533 / % possible obs: 98.4 % / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Rmerge(I) obs: 0.077
Reflection
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 10 Å / Num. obs: 11516 / Num. measured all: 73694 / Rmerge(I) obs: 0.077

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Processing

Software
NameClassification
ARP/wARPmodel building
PROLSQrefinement
SFALLrefinement
PROTINrefinement
DENZOdata reduction
RefinementResolution: 1.85→10 Å / σ(F): 1 /
RfactorNum. reflection
Rfree0.215 -
obs0.164 11516
Displacement parametersBiso mean: 29 Å2
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms927 0 0 137 1064
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it1.412
X-RAY DIFFRACTIONo_mcangle_it2.163
X-RAY DIFFRACTIONo_scbond_it7.828
X-RAY DIFFRACTIONo_scangle_it11.2510
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.0160.02
X-RAY DIFFRACTIONo_angle_d0.040.04
X-RAY DIFFRACTIONo_planar_d0.0390.04
X-RAY DIFFRACTIONo_plane_restr0.0110.02
X-RAY DIFFRACTIONo_chiral_restr0.1050.12

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