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- PDB-1gr7: Crystal structure of the double mutant Cys3Ser/Ser100Pro from Pse... -

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Basic information

Entry
Database: PDB / ID: 1gr7
TitleCrystal structure of the double mutant Cys3Ser/Ser100Pro from Pseudomonas Aeruginosa at 1.8 A resolution
ComponentsAZURIN
KeywordsELECTRON TRANSPORT
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOkvist, M. / Bonander, N. / Sandberg, A. / Karlsson, B.G. / Krengel, U. / Xue, Y. / Sjolin, L.
CitationJournal: Biochim.Biophys.Acta / Year: 2002
Title: Crystal structure of the double azurin mutant Cys3Ser/Ser100Pro from Pseudomonas aeruginosa at 1.8 A resolution: its folding-unfolding energy and unfolding kinetics.
Authors: Okvist, M. / Bonander, N. / Sandberg, A. / Karlsson, B.G. / Krengel, U. / Xue, Y. / Sjolin, L.
History
DepositionDec 14, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: citation / pdbx_database_status / struct_conn
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)56,1418
Polymers55,8874
Non-polymers2544
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.790, 100.120, 106.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.940127, 0.167037, -0.297086), (-0.17477, -0.984609, -0.000541), (-0.292604, 0.051413, 0.95485)39.2639, 96.7573, 7.2322
2given(0.938324, -0.169126, 0.301571), (-0.176749, -0.984254, -0.00204), (0.297167, -0.051388, -0.953441)1.4947, 103.4113, 49.5777
3given(-0.999988, 0.004007, 0.002845), (0.004006, 0.999992, -0.000418), (-0.002847, -0.000406, -0.999996)23.9305, -0.0621, 51.7523
DetailsTHE MOLECULE FUNCTIONS AS A MONOMER

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Components

#1: Protein
AZURIN


Mass: 13971.771 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: OXIDIZED CYSTEINE AT POSITION 26. / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / 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.: 175 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsENGINEERED MUTATIONS C3S,S100P

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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: 45 %
Crystal growpH: 5.5
Details: 3.2 M AMMONIUM SULPHATE, 1.0 M LITHIUM NITRATE, 0.2 M ACETATE BUFFER PH 5.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
13.2 Mammonium sulfate1reservoir
21.0 M1reservoirLiNO3
30.2 Macetate1reservoirpH5.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MSC / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 248852 / % possible obs: 89.2 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.2 / % possible all: 53.7
Reflection
*PLUS
Num. obs: 42969 / Num. measured all: 248852
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 53.7 % / Mean I/σ(I) obs: 2.1

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→72.55 Å / SU B: 5.68947 / SU ML: 0.16785 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.12985 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20751 2039 5 %RANDOM
Rwork0.17488 ---
obs0.17651 38652 84.5 %-
Refinement stepCycle: LAST / Resolution: 1.8→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3856 0 4 175 4035
Refinement
*PLUS
Lowest resolution: 72.5 Å / % reflection Rfree: 5 % / Rfactor obs: 0.175 / Rfactor Rfree: 0.208 / Rfactor Rwork: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.74

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