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- PDB-6iav: CO-AZURIN FROM PSEUDOMONAS AERUGINOSA TREATED WITH HYDROSULFIDE -

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Basic information

Entry
Database: PDB / ID: 6iav
TitleCO-AZURIN FROM PSEUDOMONAS AERUGINOSA TREATED WITH HYDROSULFIDE
ComponentsAzurin
KeywordsELECTRON TRANSPORT / COBALT 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 / 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
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionNov 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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
Revision 1.2Oct 9, 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)55,91911
Polymers55,5634
Non-polymers3567
Water52229
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9903
Polymers13,8911
Non-polymers992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9903
Polymers13,8911
Non-polymers992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9903
Polymers13,8911
Non-polymers992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9502
Polymers13,8911
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.429, 59.950, 82.520
Angle α, β, γ (deg.)90.00, 90.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 2 - 128 / Label seq-ID: 1 - 127

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Azurin


Mass: 13890.722 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 BL21 (bacteria) / References: UniProt: P00282
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.24 Å3/Da / Density % sol: 45.21 % / Description: TRAPEZOIDAL PLATES
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 4000, 100 MM TRIS PH 7.5, 200 MM CACL2, 10 MM NA2S. CRYOPROTECTANT: 10% PEG 4000, 20% PEG 400, 100 MM TRIS PH 7.5, 200 MM CACL2, PH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.6039 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 2, 2017 / Details: Si111
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6039 Å / Relative weight: 1
ReflectionResolution: 2→50.48 Å / Num. obs: 31819 / % possible obs: 95.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 32.9 Å2 / Rsym value: 0.09 / Net I/σ(I): 6.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2242 / Rsym value: 0.464 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GYI

6gyi


Resolution: 2→50.48 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.913 / SU B: 26.746 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.228 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30955 1563 4.9 %RANDOM
Rwork0.2496 ---
obs0.25264 30604 96.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.296 Å2
Baniso -1Baniso -2Baniso -3
1--3.81 Å2-0 Å2-1.9 Å2
2--4.07 Å20 Å2
3----0.23 Å2
Refinement stepCycle: 1 / Resolution: 2→50.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3845 0 7 29 3881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0133961
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173591
X-RAY DIFFRACTIONr_angle_refined_deg2.7371.6355357
X-RAY DIFFRACTIONr_angle_other_deg1.5751.5858415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1925518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.08726170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.65315707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.355154
X-RAY DIFFRACTIONr_chiral_restr0.1260.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.024425
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02724
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_it3.082.3672042
X-RAY DIFFRACTIONr_mcbond_other3.0762.3642041
X-RAY DIFFRACTIONr_mcangle_it4.6893.532549
X-RAY DIFFRACTIONr_mcangle_other4.693.5332550
X-RAY DIFFRACTIONr_scbond_it3.3532.5521919
X-RAY DIFFRACTIONr_scbond_other3.3522.5541920
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9843.7062802
X-RAY DIFFRACTIONr_long_range_B_refined6.9527.3034147
X-RAY DIFFRACTIONr_long_range_B_other6.95327.3194147
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A38550.11
12B38550.11
21A39110.09
22C39110.09
31A38610.12
32D38610.12
41B38430.1
42C38430.1
51B38390.12
52D38390.12
61C38670.1
62D38670.1
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 120 -
Rwork0.425 2152 -
obs--93.42 %
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)
12.9929-0.8261-1.20632.52431.48286.6880.2947-0.29130.0092-0.46860.1379-0.1282-0.60280.2366-0.43270.1916-0.070.16790.0424-0.07040.3786-4.01731.73580.089
21.9052-0.81640.13327.1967-1.98013.00940.60320.6178-0.1620.3587-0.80210.61250.01010.57530.19880.27420.12640.09450.3877-0.19270.427513.85730.54554.495
32.7010.12550.38392.15880.48168.77060.1584-0.48390.0397-0.03780.1601-0.13590.4726-0.0917-0.31850.0477-0.03660.0140.1244-0.09360.323221.17727.18995.379
44.33010.08724.58262.87370.554111.98760.2452-0.0476-0.4326-0.30560.0955-0.02460.03910.2479-0.34070.0732-0.01410.0490.01660.0290.3029-11.10127.61738.824
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 130
2X-RAY DIFFRACTION2B2 - 130
3X-RAY DIFFRACTION3C2 - 130
4X-RAY DIFFRACTION4D2 - 130

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