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- PDB-2iwe: Structure of a cavity mutant (H117G) of Pseudomonas aeruginosa azurin -

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Basic information

Entry
Database: PDB / ID: 2iwe
TitleStructure of a cavity mutant (H117G) of Pseudomonas aeruginosa azurin
ComponentsAZURIN
KeywordsELECTRON TRANSPORT / BLUE COPPER PROTEIN / REDOX PROTEIN / METAL-BINDING / AZURIN / TRANSPORT / PERIPLASMIC
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
1,1'-HEXANE-1,6-DIYLBIS(1H-IMIDAZOLE) / Azurin
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsDe Jongh, T.E. / Van Roon, A.M.M. / Prudencio, M. / Ubbink, M. / Canters, G.W.
CitationJournal: Eur.J.Inorg.Chem. / Year: 2006
Title: Click-Chemistry with an Active Site Variant of Azurin
Authors: De Jongh, T.E. / Van Roon, A.M.M. / Prudencio, M. / Ubbink, M. / Canters, G.W.
History
DepositionJun 29, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 28, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description
Revision 1.3May 30, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_label_asym_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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AZURIN
D: AZURIN
G: AZURIN
J: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,22110
Polymers55,5234
Non-polymers6986
Water543
1
A: AZURIN
J: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1115
Polymers27,7612
Non-polymers3493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-81.5 kcal/mol
Surface area12340 Å2
MethodPISA
2
D: AZURIN
G: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1115
Polymers27,7612
Non-polymers3493
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-81.4 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.664, 49.718, 66.065
Angle α, β, γ (deg.)109.25, 94.96, 99.24
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31G
41J

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 1 / Auth seq-ID: 1 - 114 / Label seq-ID: 1 - 114

Dom-IDAuth asym-IDLabel asym-ID
1AA
2DB
3GC
4JD

NCS oper:
IDCodeMatrixVector
1given(0.575, 0.324, 0.751), (0.271, 0.791, -0.549), (-0.772, 0.519, 0.367)10.184, -10.517, 29.049
2given(-0.712, -0.216, 0.669), (-0.179, -0.865, -0.469), (0.679, -0.454, 0.577)-24.13135, -21.849, 3.5338
3given(0.038, -0.723, 0.689), (-0.732, -0.49, -0.474), (0.68, -0.487, -0.548)-7.38483, -36.93147, 37.0815

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Components

#1: Protein
AZURIN


Mass: 13880.704 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: DIMERIZED BY COORDINATION OF A BIFUNCTIONAL LIGAND WIRE 1,6-DI(IMIDAZOL-1-YL)HEXANE
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PGK22 (PUC18 DERIVED) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: P00282
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-2IH / 1,1'-HEXANE-1,6-DIYLBIS(1H-IMIDAZOLE) / 1,6-DI(IMIDAZOL-1-YL)HEXANE


Mass: 218.298 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Compound detailsAZURIN, FOUND IN BACTERIA, IS THOUGHT TO TRANSFER ELECTRONS FROM CYTOCHROME C551 TO CYTOCHROME ...AZURIN, FOUND IN BACTERIA, IS THOUGHT TO TRANSFER ELECTRONS FROM CYTOCHROME C551 TO CYTOCHROME OXIDASE. ENGINEERED RESIDUE IN CHAIN A, HIS 137 TO GLY ENGINEERED RESIDUE IN CHAIN D, HIS 137 TO GLY ENGINEERED RESIDUE IN CHAIN G, HIS 137 TO GLY ENGINEERED RESIDUE IN CHAIN J, HIS 137 TO GLY
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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 8.5
Details: 100 MM TRIS-HCL PH 8.5 AND 20% (W/V) POLYETHYLENE GLYCOL (PEG) 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR78 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 9, 2004 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.85→60 Å / Num. obs: 10566 / % possible obs: 88.2 % / Observed criterion σ(I): 1.8 / Redundancy: 2.7 % / Biso Wilson estimate: 62.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.4
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.8 / % possible all: 36

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E67

1e67


Resolution: 2.83→61.66 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.908 / SU B: 44.56 / SU ML: 0.378 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE LOOP COMPRISING RESIDUES 116-121 IN CHAIN A IS MODELED IN A DOUBLE CONFORMATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 494 4.75 %RANDOM
Rwork0.192 ---
obs0.194 10566 88.2 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.791 Å2-3.624 Å2-0.822 Å2
2---1.062 Å20.363 Å2
3---0.786 Å2
Refinement stepCycle: LAST / Resolution: 2.83→61.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3872 0 36 3 3911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224026
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.071.9655409
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8665515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46926.585164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.9115710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.491154
X-RAY DIFFRACTIONr_chiral_restr0.0770.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022976
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.31803
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.52758
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.5209
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3160.337
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.54322620
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.44534108
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.46421546
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.11731301
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 873 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.090.05
2Dtight positional0.080.05
3Gtight positional0.130.05
4Jtight positional0.080.05
1Atight thermal0.170.5
2Dtight thermal0.140.5
3Gtight thermal0.140.5
4Jtight thermal0.160.5
LS refinement shellResolution: 2.83→2.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.45 14
Rwork0.33 340
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)
18.16595.6861-0.00698.85480.56172.670.1118-0.09760.34310.0315-0.13390.45980.18660.07530.0221-0.27390.19280.0587-0.25620.0004-0.15540.3890.363-0.077
25.51341.8956-1.17024.4223-1.39213.7302-0.18570.28330.0359-0.27620.24210.214-0.07030.0585-0.05640.2803-0.3368-0.09370.13450.0602-0.243810.487-10.08728.86
33.53441.8854-0.73228.0482-0.75155.2819-0.45280.288-0.0288-0.56480.5789-0.37330.25570.1188-0.12610.0415-0.191-0.06780.04920.0036-0.2126-7.65-37.3437.186
47.02386.0082-1.09529.4009-1.57362.18680.2571-0.33691.010.4807-0.3651.515-0.14780.06870.1079-0.22630.15380.1258-0.1995-0.15640.3943-24.743-22.5343.517
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 128
2X-RAY DIFFRACTION2D1 - 128
3X-RAY DIFFRACTION3G1 - 128
4X-RAY DIFFRACTION4J1 - 128

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