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- PDB-2hx7: Crystal structure of Cu(II) Azurin with the metal-binding loop se... -

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Basic information

Entry
Database: PDB / ID: 2hx7
TitleCrystal structure of Cu(II) Azurin with the metal-binding loop sequence "CTFPGHSALM" replaced with "CSPHQGAGM"
ComponentsAzurin
KeywordsELECTRON TRANSPORT / BLUE COPPER-BINDING PROTEIN / GREEK-KEY BETA-BARREL / LOOP MUTAGENESIS
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: 1.55 Å
AuthorsBanfield, M.J.
Citation
Journal: J.Am.Chem.Soc. / Year: 2007
Title: Engineering Copper Sites in Proteins: Loops Confer Native Structures and Properties to Chimeric Cupredoxins.
Authors: Li, C. / Banfield, M.J. / Dennison, C.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Basic requirements for a metal-binding site in a protein: The influence of loop shorteneing on the cupredoxin azurin
Authors: Chan, L. / Yanagisawa, S. / Martins, B.M. / Messerschmidt, A. / Banfield, M.J. / Dennison, C.
History
DepositionAug 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_site
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_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.pdbx_dist_value / _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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Azurin
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6984
Polymers27,5712
Non-polymers1272
Water8,467470
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8492
Polymers13,7861
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8492
Polymers13,7861
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.989, 65.276, 97.909
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Azurin


Mass: 13785.544 Da / Num. of mol.: 2
Mutation: Metal binding loop "CTFPGHSALM" mutated to "CSPHQGAGM"
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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 29-31% PEG 4000, 100mM magnesium chloride, 100mM Sodium acetate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 8, 2006 / Details: Osmic "blue"
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.54→54.313 Å / Num. obs: 36537 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 9.6
Reflection shellResolution: 1.54→1.62 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 2 / Num. measured all: 19172 / Num. unique all: 4673 / Rsym value: 0.341 / % possible all: 86

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å23.36 Å
Translation2.5 Å23.36 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4AZU, with residues 112-121 removed

4azu


Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.812 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, UT NOT OUTPUT TO THE FILE
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1810 5 %RANDOM
Rwork0.144 ---
all0.147 ---
obs0.147 36219 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.984 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 2 470 2376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211946
X-RAY DIFFRACTIONr_bond_other_d0.0020.021266
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.9412650
X-RAY DIFFRACTIONr_angle_other_deg0.9333.0033113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3655266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65126.66784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.83415324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.939152
X-RAY DIFFRACTIONr_chiral_restr0.1110.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022234
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02350
X-RAY DIFFRACTIONr_nbd_refined0.2120.2398
X-RAY DIFFRACTIONr_nbd_other0.1950.21289
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2969
X-RAY DIFFRACTIONr_nbtor_other0.0870.2925
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2291
X-RAY DIFFRACTIONr_metal_ion_refined0.0030.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1020.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.236
X-RAY DIFFRACTIONr_mcbond_it1.6981.51643
X-RAY DIFFRACTIONr_mcbond_other0.6181.5527
X-RAY DIFFRACTIONr_mcangle_it2.10922042
X-RAY DIFFRACTIONr_scbond_it3.2093763
X-RAY DIFFRACTIONr_scangle_it4.2064.5600
X-RAY DIFFRACTIONr_rigid_bond_restr1.56133869
X-RAY DIFFRACTIONr_sphericity_free8.0843472
X-RAY DIFFRACTIONr_sphericity_bonded3.24933170
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 127 -
Rwork0.271 2379 -
obs-2506 94.25 %

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