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- PDB-1xb3: The D62C/K74C double mutant of Pseudomonas Aeruginosa Azurin -

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Basic information

Entry
Database: PDB / ID: 1xb3
TitleThe D62C/K74C double mutant of Pseudomonas Aeruginosa Azurin
ComponentsAzurin
KeywordsELECTRON TRANSPORT / Azurin / Thermostability / Mutant
Function / homology
Function and homology information


transition metal ion binding / periplasmic space / electron transfer activity / copper ion binding / zinc ion binding / identical protein binding
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 / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å
AuthorsTigerstrom, A. / Schwarz, F. / Karlsson, G. / Okvist, M. / Alvarez-Rua, C. / Maeder, D. / Robb, F.T. / Sjolin, L.
CitationJournal: Biochemistry / Year: 2004
Title: Effects of a novel disulfide bond and engineered electrostatic interactions on the thermostability of azurin
Authors: Tigerstrom, A. / Schwarz, F. / Karlsson, G. / Okvist, M. / Alvarez-Rua, C. / Maeder, D. / Robb, F.T. / Sjolin, L.
History
DepositionAug 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_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 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Azurin
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8314
Polymers27,7042
Non-polymers1272
Water3,927218
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9152
Polymers13,8521
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9152
Polymers13,8521
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.412, 87.338, 31.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-1066-

HOH

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Components

#1: Protein Azurin


Mass: 13851.756 Da / Num. of mol.: 2 / Mutation: D62C/K74C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: AZU / Production host: Escherichia coli (E. coli) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20-23% PEG 3350, 0.25M MgCl2, 0.1M Sodium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.996 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 10, 2003
RadiationMonochromator: MIRRORS and Si 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.996 Å / Relative weight: 1
ReflectionResolution: 1.5→59.76 Å / Num. all: 36530 / Num. obs: 35091 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 24.53
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 7 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 10.1 / Num. unique all: 3663 / % possible all: 90.5

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Processing

Software
NameVersionClassification
MAR345data collection
XDSdata reduction
AMoREphasing
REFMAC5.2refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AZU

4azu


Resolution: 1.501→59.76 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.042 / SU ML: 0.052 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.098 / ESU R Free: 0.082 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21423 1823 5 %RANDOM
Rwork0.1697 ---
all0.17185 ---
obs0.17185 34706 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.366 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.61 Å20 Å2
3---0.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.082 Å0.098 Å
Refinement stepCycle: LAST / Resolution: 1.501→59.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 2 218 2163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221984
X-RAY DIFFRACTIONr_bond_other_d0.0010.021727
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9452685
X-RAY DIFFRACTIONr_angle_other_deg0.80534067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6115260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72326.29681
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65215344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.313152
X-RAY DIFFRACTIONr_chiral_restr0.0920.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022238
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02362
X-RAY DIFFRACTIONr_nbd_refined0.2030.2401
X-RAY DIFFRACTIONr_nbd_other0.1780.21707
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2988
X-RAY DIFFRACTIONr_nbtor_other0.0860.21183
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2136
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0110.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3160.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.7041.51640
X-RAY DIFFRACTIONr_mcbond_other0.6631.5539
X-RAY DIFFRACTIONr_mcangle_it2.10822059
X-RAY DIFFRACTIONr_scbond_it2.9713811
X-RAY DIFFRACTIONr_scangle_it3.9954.5626
X-RAY DIFFRACTIONr_rigid_bond_restr1.62634390
X-RAY DIFFRACTIONr_sphericity_free8.3963220
X-RAY DIFFRACTIONr_sphericity_bonded3.82433670
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 121 -
Rwork0.174 2388 -
obs--96.2 %

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