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- PDB-2ft7: Structure of Cu(I)azurin at pH 6, with the metal-binding loop seq... -

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Basic information

Entry
Database: PDB / ID: 2ft7
TitleStructure of Cu(I)azurin at pH 6, with the metal-binding loop sequence "CTFPGHSALM" replaced with "CTPHPM"
ComponentsAzurin
KeywordsELECTRON TRANSPORT / Blue copper-binding protein / 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. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (I) ION / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Direct refinement using refined AZAMI-F Cu(II) structure / Resolution: 1.4 Å
AuthorsBanfield, M.J.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Basic requirements for a metal-binding site in a protein: The influence of loop shortening on the cupredoxin azurin.
Authors: Li, C. / Yanagisawa, S. / Martins, B.M. / Messerschmidt, A. / Banfield, M.J. / Dennison, C.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Crystal structure analysis of oxidized Pseudomonas aeruginosa azurin at pH 5.5 and pH 9.0. A pH-induced conformational transition involves a peptide bond flip
Authors: Nar, H. / Messerschmidt, A. / Huber, R. / van de Kamp, M. / Canters, G.W.
#2: Journal: J.Am.Chem.Soc. / Year: 2004
Title: Loop-contraction mutagenesis of type 1 copper sites
Authors: Yanagisawa, S. / Dennison, C.
#3: Journal: J.Mol.Biol. / Year: 1994
Title: Crystal structure analysis and refinement at 2.15 A resolution of amicyanin, a type I blue copper protein, from Thiobacillus versutus
Authors: Romero, A. / Nar, H. / Huber, R. / Messerschmidt, A. / Kalverda, A.P. / Canters, G.W. / Durley, R. / Mathews, F.S.
History
DepositionJan 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 20, 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 / struct_conn / struct_site
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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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
Remark 999Amino acid sequence CTFPGHSALM, involving residues 132 to 141 in the amino acid database was ...Amino acid sequence CTFPGHSALM, involving residues 132 to 141 in the amino acid database was replaced with the sequence CTPHPM in the deposition

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6472
Polymers13,5831
Non-polymers641
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.957, 51.957, 75.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is monomeric (as found in the asymmetric unit)

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Components

#1: Protein Azurin


Mass: 13583.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: azu / Plasmid: Trk99a / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P00282
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 1.87 Å3/Da / Density % sol: 34.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1MM MES, 20% PEG6000, 0.2M LiCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.075 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 16, 2005
RadiationMonochromator: Double SI(III) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.4→42.8 Å / Num. all: 29159 / Num. obs: 29159 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 24.9
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 6.7 / Num. unique all: 2999 / Rsym value: 0.324 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: Direct refinement using refined AZAMI-F Cu(II) structure
Resolution: 1.4→42.8 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.977 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.068 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS BUT NOT PRESENT IN OUTPUT FILE
RfactorNum. reflection% reflectionSelection details
Rfree0.178 1045 5 %RANDOM
Rwork0.139 ---
all0.141 20853 --
obs0.141 20853 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.252 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2---0.48 Å20 Å2
3---0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.4→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms965 0 2 164 1131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021994
X-RAY DIFFRACTIONr_bond_other_d0.0010.02871
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.951368
X-RAY DIFFRACTIONr_angle_other_deg0.87632051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5665141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.86926.42942
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.66315169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.181151
X-RAY DIFFRACTIONr_chiral_restr0.1140.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021142
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02178
X-RAY DIFFRACTIONr_nbd_refined0.2440.2195
X-RAY DIFFRACTIONr_nbd_other0.1890.2882
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2494
X-RAY DIFFRACTIONr_nbtor_other0.090.2572
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.291
X-RAY DIFFRACTIONr_metal_ion_refined0.0170.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.219
X-RAY DIFFRACTIONr_mcbond_it2.1821.5682
X-RAY DIFFRACTIONr_mcbond_other1.1871.5262
X-RAY DIFFRACTIONr_mcangle_it2.84921047
X-RAY DIFFRACTIONr_scbond_it3.8283383
X-RAY DIFFRACTIONr_scangle_it4.8154.5312
X-RAY DIFFRACTIONr_rigid_bond_restr1.7532034
X-RAY DIFFRACTIONr_sphericity_free11.5193166
X-RAY DIFFRACTIONr_sphericity_bonded6.97331836
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.173 70 -
Rwork0.148 1427 -
obs-1497 100 %

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