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- PDB-1xb8: Zn substituted form of D62C/K74C double mutant of Pseudomonas Aer... -

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Basic information

Entry
Database: PDB / ID: 1xb8
TitleZn substituted form of 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
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 30, 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: Advisory / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 20, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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
C: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9784
Polymers27,8482
Non-polymers1312
Water3,243180
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9892
Polymers13,9241
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9892
Polymers13,9241
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.140, 50.038, 57.722
Angle α, β, γ (deg.)90.00, 119.51, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein Azurin


Mass: 13923.817 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.55 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Ammonium Sulfate, 0.1 M Cacodylate, 30% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Jan 27, 2004 / Details: Osmic mirror
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50.25 Å / Num. all: 18766 / Num. obs: 18766 / % possible obs: 99.8 % / Observed criterion σ(I): -3.7 / Redundancy: 4.04 % / Biso Wilson estimate: 20.44295 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.2
Reflection shellResolution: 2→2.15 Å / Redundancy: 4.03 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.06 / Num. unique all: 3302 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.2refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AZU

1azu


Resolution: 2→50.25 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.423 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.163 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23562 963 5 %RANDOM
Rwork0.19208 ---
all0.19428 18145 --
obs0.19428 18145 99.73 %-
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: 16.846 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å2-0.16 Å2
2--0.91 Å20 Å2
3----0.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.163 Å0.182 Å
Refinement stepCycle: LAST / Resolution: 2→50.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1913 0 2 180 2095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221955
X-RAY DIFFRACTIONr_bond_other_d0.0010.021710
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.9492640
X-RAY DIFFRACTIONr_angle_other_deg0.86334028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9915251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70826.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63215347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.309152
X-RAY DIFFRACTIONr_chiral_restr0.1080.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022171
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02353
X-RAY DIFFRACTIONr_nbd_refined0.2010.2420
X-RAY DIFFRACTIONr_nbd_other0.190.21716
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2956
X-RAY DIFFRACTIONr_nbtor_other0.0910.21127
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2138
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1760.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0451.51600
X-RAY DIFFRACTIONr_mcbond_other0.1941.5525
X-RAY DIFFRACTIONr_mcangle_it1.22822014
X-RAY DIFFRACTIONr_scbond_it2.0453803
X-RAY DIFFRACTIONr_scangle_it2.8814.5626
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 74 -
Rwork0.217 1306 -
obs--99.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2273-0.3633-0.47570.93280.11391.5415-0.1832-0.0084-0.0716-0.0330.11880.0636-0.0061-0.0610.06440.02540.01260.00110.15520.00880.008332.7180.2636.016
21.47210.398-0.56531.0987-0.25630.7209-0.1234-0.3729-0.0665-0.1208-0.0169-0.06520.10980.15150.1403-0.03550.08840.03310.29280.0457-0.04065.60716.07717.881
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1282 - 128
2X-RAY DIFFRACTION1AC10011
3X-RAY DIFFRACTION2CB3 - 1283 - 128
4X-RAY DIFFRACTION2CD50011

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