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- PDB-5syd: Circularly permutated azurin (cpAz) based on P. aeruginosa azurin... -

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Basic information

Entry
Database: PDB / ID: 5syd
TitleCircularly permutated azurin (cpAz) based on P. aeruginosa azurin sequence
ComponentsAzurin, chimeric construct
KeywordsOXIDOREDUCTASE / cupredoxin / engineered / greek-key beta barrel
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. / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / Azurin / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.397 Å
AuthorsPetrik, I. / Yang, Y. / Howard, R. / Yi, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: Circular Permutation of Azurin Results in the same Type 1 Blue Copper with different Reduction Potentials
Authors: Yu, Y. / Petrik, I. / Chacon, K.N. / Hosseinzadeh, P. / Blackburn, N. / Yi, L.
History
DepositionAug 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: 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 / struct_ncs_dom_lim
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.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_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 1.3Nov 20, 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, chimeric construct
B: Azurin, chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4106
Polymers28,1562
Non-polymers2544
Water97354
1
A: Azurin, chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2694
Polymers14,0781
Non-polymers1913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Azurin, chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1412
Polymers14,0781
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.436, 115.436, 83.145
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 4:62 or resseq 64:87 or resseq 97:117 or resseq 120:129))
21(chain B and (resseq 4:62 or resseq 64:87 or resseq 97:117 or resseq 120:129))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLEULEU(chain A and (resseq 4:62 or resseq 64:87 or resseq 97:117 or resseq 120:129))AA4 - 624 - 62
12GLUGLULEULEU(chain A and (resseq 4:62 or resseq 64:87 or resseq 97:117 or resseq 120:129))AA64 - 8764 - 87
13SERSERLYSLYS(chain A and (resseq 4:62 or resseq 64:87 or resseq 97:117 or resseq 120:129))AA97 - 11797 - 117
14LYSLYSPROPRO(chain A and (resseq 4:62 or resseq 64:87 or resseq 97:117 or resseq 120:129))AA120 - 129120 - 129
21METMETLEULEU(chain B and (resseq 4:62 or resseq 64:87 or resseq 97:117 or resseq 120:129))BB4 - 624 - 62
22GLUGLULEULEU(chain B and (resseq 4:62 or resseq 64:87 or resseq 97:117 or resseq 120:129))BB64 - 8764 - 87
23SERSERLYSLYS(chain B and (resseq 4:62 or resseq 64:87 or resseq 97:117 or resseq 120:129))BB97 - 11797 - 117
24LYSLYSPROPRO(chain B and (resseq 4:62 or resseq 64:87 or resseq 97:117 or resseq 120:129))BB120 - 129120 - 129

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Components

#1: Protein Azurin, chimeric construct


Mass: 14077.919 Da / Num. of mol.: 2 / Fragment: unp residues 63-148; 1-38
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: azu, PA4922 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00282, UniProt: B3EWN9
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 5.68 Å3/Da / Density % sol: 78.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 2 uL of 5 mM protein was mixed with equal amount of well buffer (0.1 M Tris, 0.1 M LiNO 3, 0.01 M CUSO 4 with 35% polyethylene glycol 10000), and crystalized using the hanging drop method, ...Details: 2 uL of 5 mM protein was mixed with equal amount of well buffer (0.1 M Tris, 0.1 M LiNO 3, 0.01 M CUSO 4 with 35% polyethylene glycol 10000), and crystalized using the hanging drop method, with 300 uL well buffer in the crystallization tray.
PH range: 7.5-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.397→50 Å / Num. obs: 25321 / % possible obs: 99.7 % / Redundancy: 23.5 % / Biso Wilson estimate: 61.35 Å2 / Rmerge(I) obs: 0.1 / Net I/av σ(I): 39.44 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.4917.80.674197.9
2.49-2.5919.80.575199.6
2.59-2.721.60.4491100
2.7-2.85220.3331100
2.85-3.0222.10.2351100
3.02-3.2622.10.1711100
3.26-3.58220.1111100
3.58-4.123.50.1021100
4.1-5.1732.10.0971100
5.17-5030.80.071100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
Cootmodel building
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AZU

4azu


Resolution: 2.397→42.84 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2512 1289 5.1 %
Rwork0.2235 23992 -
obs0.2249 25281 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.69 Å2 / Biso mean: 73.2389 Å2 / Biso min: 38.84 Å2
Refinement stepCycle: final / Resolution: 2.397→42.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 4 54 2012
Biso mean--71.18 68.36 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052072
X-RAY DIFFRACTIONf_angle_d0.962798
X-RAY DIFFRACTIONf_chiral_restr0.056310
X-RAY DIFFRACTIONf_plane_restr0.005368
X-RAY DIFFRACTIONf_dihedral_angle_d14.1691240
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A996X-RAY DIFFRACTION10.865TORSIONAL
12B996X-RAY DIFFRACTION10.865TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3973-2.49320.44781350.41542509264495
2.4932-2.60670.36351630.346626022765100
2.6067-2.74410.32221450.316326672812100
2.7441-2.9160.31841210.313326532774100
2.916-3.14110.33411500.287726692819100
3.1411-3.45710.28311320.25226922824100
3.4571-3.9570.29051600.234526832843100
3.957-4.98420.19951510.180126832834100
4.9842-42.84650.19591320.172928342966100

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