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- PDB-2hx8: Crystal structure of Cu(I) Azurin with the metal-binding loop seq... -

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Basic information

Entry
Database: PDB / ID: 2hx8
TitleCrystal structure of Cu(I) Azurin with the metal-binding loop sequence "CTFPGHSALM" replaced with "CSPHQGAGM", at pH5
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 (I) ION / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Direct use of Oxidised structure in same crystal form / Resolution: 1.6 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 1.3Apr 3, 2024Group: 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
Water8,071448
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)38.905, 65.345, 97.707
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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
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.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.25 Å3/Da / Density % sol: 45.37 %
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 13, 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: 1.547→54.317 Å / Num. obs: 33470 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 10.2
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 2.4 / Num. measured all: 31142 / Num. unique all: 4783 / Rsym value: 0.302 / % possible all: 99

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: Direct use of Oxidised structure in same crystal form
Starting model: Cu(II) form of the protein

Resolution: 1.6→54.31 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.821 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, BUT NOT OUTPUT TO FINAL FILE
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1667 5 %RANDOM
Rwork0.138 ---
all0.14 ---
obs0.14 33411 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.285 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.97 Å20 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.6→54.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 2 448 2352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211944
X-RAY DIFFRACTIONr_bond_other_d0.0010.021271
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.9432646
X-RAY DIFFRACTIONr_angle_other_deg0.9253.0033126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.2365266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25426.54381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.91615327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.045152
X-RAY DIFFRACTIONr_chiral_restr0.1020.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022222
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02350
X-RAY DIFFRACTIONr_nbd_refined0.2020.2385
X-RAY DIFFRACTIONr_nbd_other0.1910.21285
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2942
X-RAY DIFFRACTIONr_nbtor_other0.0870.2964
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2254
X-RAY DIFFRACTIONr_metal_ion_refined0.0020.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1150.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.233
X-RAY DIFFRACTIONr_mcbond_it1.5951.51649
X-RAY DIFFRACTIONr_mcbond_other0.5771.5527
X-RAY DIFFRACTIONr_mcangle_it1.95622043
X-RAY DIFFRACTIONr_scbond_it2.9663761
X-RAY DIFFRACTIONr_scangle_it3.9454.5595
X-RAY DIFFRACTIONr_rigid_bond_restr1.44833878
X-RAY DIFFRACTIONr_sphericity_free8.0933450
X-RAY DIFFRACTIONr_sphericity_bonded3.33633173
LS refinement shellResolution: 1.603→1.644 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 128 -
Rwork0.203 2270 -
obs-2398 98.08 %

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