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- PDB-5i26: Azurin T30R1, crystal form I -

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Basic information

Entry
Database: PDB / ID: 5i26
TitleAzurin T30R1, crystal form I
ComponentsAzurin
KeywordsMETAL BINDING PROTEIN / blue copper protein / spin label
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
COPPER (II) ION / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.888 Å
AuthorsHagelueken, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationCRC 813, A6 Germany
CitationJournal: Phys Chem Chem Phys / Year: 2016
Title: Determination of nitroxide spin label conformations via PELDOR and X-ray crystallography.
Authors: Abdullin, D. / Hagelueken, G. / Schiemann, O.
History
DepositionFeb 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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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)56,8478
Polymers56,5924
Non-polymers2544
Water5,531307
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2122
Polymers14,1481
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2122
Polymers14,1481
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2122
Polymers14,1481
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2122
Polymers14,1481
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.560, 68.750, 93.440
Angle α, β, γ (deg.)90.00, 96.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Azurin


Mass: 14148.116 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.8943 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8943 Å / Relative weight: 1
ReflectionResolution: 1.888→37.361 Å / Num. obs: 39652 / % possible obs: 90.41 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 61.22
Reflection shellResolution: 1.888→1.96 Å / Rmerge(I) obs: 2.78

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+67 / Resolution: 1.888→37.361 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2401 1923 4.86 %
Rwork0.1938 --
obs0.1961 39583 90.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.888→37.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3913 0 4 307 4224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084090
X-RAY DIFFRACTIONf_angle_d1.1625542
X-RAY DIFFRACTIONf_dihedral_angle_d14.9181542
X-RAY DIFFRACTIONf_chiral_restr0.048611
X-RAY DIFFRACTIONf_plane_restr0.005717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.888-1.93520.33391380.29292598X-RAY DIFFRACTION88
1.9352-1.98760.27171290.23832785X-RAY DIFFRACTION93
1.9876-2.0460.25741540.22172786X-RAY DIFFRACTION94
2.046-2.11210.28741480.21832752X-RAY DIFFRACTION93
2.1121-2.18750.27381270.20852751X-RAY DIFFRACTION93
2.1875-2.27510.29671570.20782715X-RAY DIFFRACTION92
2.2751-2.37870.25681310.19952740X-RAY DIFFRACTION92
2.3787-2.5040.26931070.21292765X-RAY DIFFRACTION92
2.504-2.66090.27691280.20142707X-RAY DIFFRACTION91
2.6609-2.86630.26851630.20812665X-RAY DIFFRACTION90
2.8663-3.15460.26091330.2022669X-RAY DIFFRACTION90
3.1546-3.61070.21361490.17532615X-RAY DIFFRACTION88
3.6107-4.54790.18971370.14952606X-RAY DIFFRACTION87
4.5479-37.36810.17291220.17282506X-RAY DIFFRACTION82

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