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- PDB-1bex: STRUCTURE OF RUTHENIUM-MODIFIED PSEUDOMONAS AERUGINOSA AZURIN -

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Basic information

Entry
Database: PDB / ID: 1bex
TitleSTRUCTURE OF RUTHENIUM-MODIFIED PSEUDOMONAS AERUGINOSA AZURIN
ComponentsAZURIN
KeywordsELECTRON TRANSPORT / AZURIN
Function / homology
Function and homology information


transition metal ion binding / periplasmic space / electron transfer activity / copper ion binding / zinc ion binding / identical protein binding / plasma membrane
Similarity search - Function
Azurin / : / 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 / RUTHEMIUM BIS(2,2'-BIPYRIDINE)-2-IMIDAZOLE / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFaham, S. / Day, M.W. / Rees, D.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Structures of ruthenium-modified Pseudomonas aeruginosa azurin and [Ru(2,2'-bipyridine)2(imidazole)2]SO4 x 10H2O.
Authors: Faham, S. / Day, M.W. / Connick, W.B. / Crane, B.R. / Di Bilio, A.J. / Schaefer, W.P. / Rees, D.C. / Gray, H.B.
History
DepositionMay 18, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AZURIN
B: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1418
Polymers27,9242
Non-polymers1,2176
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: AZURIN
hetero molecules

B: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1418
Polymers27,9242
Non-polymers1,2176
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1540 Å2
ΔGint-26 kcal/mol
Surface area12860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.600, 35.400, 74.700
Angle α, β, γ (deg.)90.00, 106.50, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.73261, -0.15783, 0.66209), (0.16674, -0.98472, -0.05024), (0.6599, 0.07359, 0.74774)
Vector: 3.471, 10.602, 5.113)

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Components

#1: Protein AZURIN


Mass: 13961.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P00282
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-RBU / RUTHEMIUM BIS(2,2'-BIPYRIDINE)-2-IMIDAZOLE


Mass: 481.515 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H20N6Ru
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growpH: 8
Details: 30% PEG 4000, 100 MM LINO3,20 MM CUCL2,100 MM TRIS PH 8.0
Crystal
*PLUS
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
2100 mM1dropNaOAc
330 %(w/v)PEG40001reservoir
4100 mM1reservoirLiNO3
520 mM1reservoirCuCl2
6100 mMTris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jul 1, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 11083 / % possible obs: 82 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.7
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.017 / Mean I/σ(I) obs: 4.2
Reflection
*PLUS
Num. all: 13540 / Num. measured all: 38571
Reflection shell
*PLUS
Rmerge(I) obs: 0.17

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
X-PLOR3.843model building
X-PLOR3.843refinement
XENGENdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AG0

1ag0


Resolution: 2.3→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: FREE R / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.289 955 8.3 %RANDOM
Rwork0.209 ---
obs0.209 9705 84.4 %-
Displacement parametersBiso mean: 12.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å24.23 Å2
2---0.29 Å20 Å2
3---1.09 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 64 92 2104
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.75
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.81
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.388 80 5.6 %
Rwork0.279 823 -
obs--63.1 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.81

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