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- PDB-1zib: REDUCED PSEUDOAZURIN -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1zib
TitleREDUCED PSEUDOAZURIN
ComponentsPSEUDOAZURIN
KeywordsELECTRON TRANSPORT / 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 speciesAchromobacter cycloclastes (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsInoue, T. / Nishio, N. / Hamanaka, S. / Shimomura, T. / Harada, S. / Suzuki, S. / Kohzuma, T. / Shidara, S. / Iwasaki, H. / Kai, Y.
CitationJournal: J.Biochem.(Tokyo) / Year: 1993
Title: Crystallization and preliminary X-ray studies on pseudoazurin from Achromobacter cycloclastes IAM1013.
Authors: Inoue, T. / Nishio, N. / Kai, Y. / Harada, S. / Ohshiro, Y. / Suzuki, S. / Kohzuma, T. / Shidara, S. / Iwasaki, H.
History
DepositionApr 9, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: 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 ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.process_site / _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_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: PSEUDOAZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0962
Polymers13,0331
Non-polymers641
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.650, 61.670, 30.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PSEUDOAZURIN


Mass: 13032.940 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: REDUCED BY ASCORBIC ACID / Source: (natural) Achromobacter cycloclastes (bacteria) / Strain: IAM1013 / References: UniProt: P19567
#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.: 92 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 40 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 Msodium cacodylate1drop
31 mMsodium azide1drop
450 %satammonium sulfate1drop
50.1 Msodium cacodylate1reservoir
61 mMsodium azide1reservoir
75 %(w/v)PEG80001reservoir
870 %satammonium sulfate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 13, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 7257 / % possible obs: 96.3 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.037

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Processing

Software
NameClassification
PROLSQrefinement
PROCESSdata reduction
RefinementResolution: 2→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.1687 -
obs-7188
Displacement parametersBiso mean: 18.45 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms913 0 1 92 1006
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0390.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0420.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.2151.5
X-RAY DIFFRACTIONp_mcangle_it1.8832
X-RAY DIFFRACTIONp_scbond_it2.8592
X-RAY DIFFRACTIONp_scangle_it4.2792.5
X-RAY DIFFRACTIONp_plane_restr0.0170.02
X-RAY DIFFRACTIONp_chiral_restr0.1940.15
X-RAY DIFFRACTIONp_singtor_nbd0.170.2
X-RAY DIFFRACTIONp_multtor_nbd0.2250.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1450.2
X-RAY DIFFRACTIONp_planar_tor3.0123
X-RAY DIFFRACTIONp_staggered_tor18.81415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor21.27720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.1687
Solvent computation
*PLUS
Displacement parameters
*PLUS

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