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- PDB-1i53: RE(I)-TRICARBONYL DIIMINE (Q107H)) AZURIN -

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Basic information

Entry
Database: PDB / ID: 1i53
TitleRE(I)-TRICARBONYL DIIMINE (Q107H)) AZURIN
ComponentsAZURIN
KeywordsELECTRON TRANSPORT / azurin / rhenium / electron transfer / tyrosyl and tryptophan radical
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 / 4,7-DIMETHYL-[1,10]PHENANTHROLINE / RHENIUM (I) TRICARBONYL / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDi Bilio, A.J. / Crane, B.R. / Wehbi, W.A. / Kiser, C.N. / Abu-Omar, M.M. / Carlos, R.M. / Richards, J.H. / Winkler, J.R. / Gray, H.B.
CitationJournal: J.Am.Chem.Soc. / Year: 2001
Title: Properties of photogenerated tryptophan and tyrosyl radicals in structurally characterized proteins containing rhenium(I) tricarbonyl diimines.
Authors: Di Bilio, A.J. / Crane, B.R. / Wehbi, W.A. / Kiser, C.N. / Abu-Omar, M.M. / Carlos, R.M. / Richards, J.H. / Winkler, J.R. / Gray, H.B.
History
DepositionFeb 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Database references / Structure summary / Category: struct / struct_ref_seq_dif / Item: _struct.title / _struct_ref_seq_dif.details
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _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.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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Oct 30, 2024Group: Non-polymer description / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.formula

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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)29,0068
Polymers27,9222
Non-polymers1,0846
Water4,306239
1
A: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5034
Polymers13,9611
Non-polymers5423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5034
Polymers13,9611
Non-polymers5423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.000, 42.870, 48.510
Angle α, β, γ (deg.)80.52, 77.69, 66.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein AZURIN


Mass: 13960.814 Da / Num. of mol.: 2 / Mutation: Q107H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: PET9A/ASA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: P00282
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-RTC / RHENIUM (I) TRICARBONYL


Mass: 270.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3O3Re
#4: Chemical ChemComp-DPT / 4,7-DIMETHYL-[1,10]PHENANTHROLINE


Mass: 208.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: CuCl2, Imidazole, LiNo3, PEG 8K, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
126 mg/mlprotein1drop
225 mMHEPES1drop
320 %PEG80001reservoir
4100 mMimidazol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 29, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 20201 / Num. obs: 45216 / % possible obs: 86 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.4
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.112 / % possible all: 83
Reflection
*PLUS
Num. all: 45216 / Num. obs: 20201

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BEX

1bex


Resolution: 1.8→24.56 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1144283.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0 / σ(I): 0
Stereochemistry target values: Engh and Huber + CSB model complex values for Re label
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1625 8 %RANDOM
Rwork0.238 ---
all0.238 20201 --
obs0.238 20201 86.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.77 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso mean: 20.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å2-2.95 Å2-0.21 Å2
2---0.55 Å24.59 Å2
3---1.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→24.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 48 239 2235
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_mcbond_it0.321.5
X-RAY DIFFRACTIONc_mcangle_it0.592
X-RAY DIFFRACTIONc_scbond_it0.292
X-RAY DIFFRACTIONc_scangle_it0.462.5
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.319 144 7.4 %
Rwork0.311 1805 -
obs--83.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM19X.HEMEWATER.TOP
X-RAY DIFFRACTION3REPHEN.PARREPHEN.TOP
X-RAY DIFFRACTION4WATER.PARAMTOPH19X.HEME
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.12
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.319 / % reflection Rfree: 7.4 % / Rfactor Rwork: 0.311

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