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- PDB-6gyi: Azurin fom Pseudomonas aeruginosa treated with hydrosulfide -

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Basic information

Entry
Database: PDB / ID: 6gyi
TitleAzurin fom Pseudomonas aeruginosa treated with hydrosulfide
ComponentsAzurin
KeywordsELECTRON TRANSPORT / copper protein / hydrosulfide sensor
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: 1.6 Å
AuthorsPalm, G.J. / Kohlhause, D.
CitationJournal: Eur J Inorg Chem / Year: 2019
Title: Azurin and HS-: towards implementation of a sensor for HS-detection.
Authors: Strianese, M. / Palm, G.J. / Kohlhause, D. / Ndamba, L.A. / Tabares, L.C. / Pellecchia , C.
History
DepositionJun 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.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.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_symmetry
Revision 1.2Nov 13, 2024Group: Structure summary / Category: 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
C: Azurin
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,26212
Polymers55,8474
Non-polymers4148
Water7,692427
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0653
Polymers13,9621
Non-polymers1042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0653
Polymers13,9621
Non-polymers1042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0653
Polymers13,9621
Non-polymers1042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0653
Polymers13,9621
Non-polymers1042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.736, 59.781, 79.727
Angle α, β, γ (deg.)90.00, 90.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Azurin


Mass: 13961.799 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: azu, PA4922 / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.18 Å3/Da / Density % sol: 44 % / Description: trapezoidal plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 4000, 100 mM NaHEPES pH 6,5, 200 mM CaCl2, 10 mM Na2S. Cryoprotectant: 10% PEG 4000, 20% PEG 400, 100 mM NaHEPES pH 6,5, 200 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.8141 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 2, 2017 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8141 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 62899 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 30 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.033 / Rrim(I) all: 0.046 / Net I/σ(I): 10.8
Reflection shellResolution: 1.59→1.69 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.015 / Mean I/σ(I) obs: 1.46 / Num. unique obs: 9844 / CC1/2: 0.646 / Rrim(I) all: 1.099 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSNov 1, 2016data reduction
XDSNov 1, 2016data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AZU

1azu


Resolution: 1.6→47.83 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.939 / Rfactor Rfree error: 0.005 / SU B: 5.794 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.105 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24273 2089 3.3 %RANDOM
Rwork0.19161 ---
obs0.1933 60454 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.679 Å2
Baniso -1Baniso -2Baniso -3
1--2.79 Å2-0 Å2-0.36 Å2
2--1.23 Å20 Å2
3---1.57 Å2
Refinement stepCycle: 1 / Resolution: 1.6→47.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3853 0 8 427 4288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0193977
X-RAY DIFFRACTIONr_bond_other_d0.0020.023604
X-RAY DIFFRACTIONr_angle_refined_deg2.7291.9495386
X-RAY DIFFRACTIONr_angle_other_deg1.30638449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1765523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.70626.407167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54115706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.03154
X-RAY DIFFRACTIONr_chiral_restr0.180.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.024454
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02722
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1791.0992050
X-RAY DIFFRACTIONr_mcbond_other1.1771.0982049
X-RAY DIFFRACTIONr_mcangle_it1.8321.642560
X-RAY DIFFRACTIONr_mcangle_other1.8321.6412561
X-RAY DIFFRACTIONr_scbond_it1.7471.2631927
X-RAY DIFFRACTIONr_scbond_other1.7471.2641928
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6171.8162818
X-RAY DIFFRACTIONr_long_range_B_refined5.99614.8194572
X-RAY DIFFRACTIONr_long_range_B_other5.92914.0254474
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0.028
RfactorNum. reflection% reflection
Rfree0.34 152 3.5 %
Rwork0.305 4388 -
obs--98.42 %
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)
12.7095-0.427-0.38581.6477-0.09840.89090.13980.51890.2419-0.0063-0.127-0.1308-0.0306-0.1173-0.01280.27030.04420.02030.22670.07870.034811.00329.30811.947
22.1293-0.58751.31781.4243-1.3053.8870.20780.0169-0.0095-0.12620.11140.19280.31790.0878-0.31920.2105-0.0024-0.05150.03220.00880.046628.62728.45337.543
32.9128-1.9824-0.19683.5579-0.32781.9916-0.3266-0.5605-0.30480.3690.47970.2459-0.1543-0.0704-0.15310.26170.09250.05160.23450.08680.05013.23333.20852.305
41.3181-0.1998-0.9882.3467-1.59753.4979-0.0493-0.03560.0518-0.08950.123-0.16170.0489-0.1476-0.07370.214-0.02260.01590.0782-0.00620.028636.41532.44-1.885
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 128
2X-RAY DIFFRACTION2B2 - 128
3X-RAY DIFFRACTION3C1 - 128
4X-RAY DIFFRACTION4D2 - 128

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