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- PDB-1bqk: OXIDIZED PSEUDOAZURIN -

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Basic information

Entry
Database: PDB / ID: 1bqk
TitleOXIDIZED 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsInoue, T. / Nishio, N. / Hamanaka, S. / Shimomura, T. / Harada, S. / Suzuki, S. / Kohzuma, T. / Shidara, S. / Iwasaki, H. / Kai, Y.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: Crystal structure determinations of oxidized and reduced pseudoazurins from Achromobacter cycloclastes. Concerted movement of copper site in redox forms with the rearrangement of hydrogen bond ...Title: Crystal structure determinations of oxidized and reduced pseudoazurins from Achromobacter cycloclastes. Concerted movement of copper site in redox forms with the rearrangement of hydrogen bond at a remote histidine.
Authors: Inoue, T. / Nishio, N. / Suzuki, S. / Kataoka, K. / Kohzuma, T. / Kai, Y.
#1: Journal: Thesis
Title: Crystal Structure Determinations of Oxidized and Reduced Pseudoazurin from Achromobacter Cycloclastes: A Redox-Induced Conformational Change Contains a Peptide Bond Flip
#2: Journal: 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
DepositionAug 17, 1998Processing site: BNL
Revision 1.0Aug 17, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.731, 61.544, 30.083
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: OXIDIZED FORM OF PSEUDOAZURIN / 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.: 121 / 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: 1.9 Å3/Da / Density % sol: 40 %
Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Inoue, T., (1993) J.Biochem.(Tokyo), 114, 761.
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

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jun 25, 1993 / Details: MIRROR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→8 Å / Num. obs: 21303 / % possible obs: 88.8 % / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 9.02 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 8
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.182 / % possible all: 56
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 222685
Reflection shell
*PLUS
Lowest resolution: 1.4 Å / % possible obs: 56 %

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PZA

1pza


Resolution: 1.35→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: ESTIMATED COORDINATE ERROR. ESD FROM LUZZATI PLOT (A) : 0.137
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1084 5 %RANDOM
Rwork0.178 ---
obs0.176 21303 88.8 %-
Displacement parametersBiso mean: 11.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.13 Å
Refinement stepCycle: LAST / Resolution: 1.35→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms913 0 1 121 1035
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.02
X-RAY DIFFRACTIONp_angle_d0.0220.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0260.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1372
X-RAY DIFFRACTIONp_mcangle_it1.73
X-RAY DIFFRACTIONp_scbond_it1.9122
X-RAY DIFFRACTIONp_scangle_it2.9373
X-RAY DIFFRACTIONp_plane_restr0.02250.03
X-RAY DIFFRACTIONp_chiral_restr0.1090.15
X-RAY DIFFRACTIONp_singtor_nbd0.1680.3
X-RAY DIFFRACTIONp_multtor_nbd0.2370.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1320.3
X-RAY DIFFRACTIONp_planar_tor47
X-RAY DIFFRACTIONp_staggered_tor12.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.820
X-RAY DIFFRACTIONp_special_tor11.215
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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