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- PDB-4qkt: Azurin mutant M121EM44K with copper -

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Basic information

Entry
Database: PDB / ID: 4qkt
TitleAzurin mutant M121EM44K with copper
ComponentsAzurin
KeywordsELECTRON TRANSPORT / 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
ACETATE ION / COPPER (II) ION / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.641 Å
AuthorsLiu, J. / Robinson, H. / Lu, Y.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Redesigning the Blue Copper Azurin into a Redox-Active Mononuclear Nonheme Iron Protein: Preparation and Study of Fe(II)-M121E Azurin.
Authors: Liu, J. / Meier, K.K. / Tian, S. / Zhang, J.L. / Guo, H. / Schulz, C.E. / Robinson, H. / Nilges, M.J. / Munck, E. / Lu, Y.
History
DepositionJun 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Oct 30, 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_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,60011
Polymers27,9152
Non-polymers6859
Water3,693205
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2705
Polymers13,9581
Non-polymers3134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3306
Polymers13,9581
Non-polymers3725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.285, 48.695, 95.068
Angle α, β, γ (deg.)90.00, 94.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Azurin


Mass: 13957.701 Da / Num. of mol.: 2 / Mutation: M121E, M44K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / 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.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8
Details: pH8.0 100mM LiNO3 100 mM Tris 25%PEG4000 1:1 mixing-medium, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.641→47.378 Å / Num. all: 60473 / Num. obs: 59197 / % possible obs: 97.89 % / Observed criterion σ(F): 1.37 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.641→47.378 Å / SU ML: 0.17 / σ(F): 1.37 / Phase error: 21.87 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 1981 6.61 %RANDOM
Rwork0.1812 ---
obs0.1834 59197 97.89 %-
all-59204 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.641→47.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 26 205 2133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071962
X-RAY DIFFRACTIONf_angle_d0.9832643
X-RAY DIFFRACTIONf_dihedral_angle_d13.595714
X-RAY DIFFRACTIONf_chiral_restr0.041297
X-RAY DIFFRACTIONf_plane_restr0.005342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6411-1.66110.25221100.22411842X-RAY DIFFRACTION89
1.6611-1.68210.23581540.21661935X-RAY DIFFRACTION96
1.6821-1.70420.25021520.20521914X-RAY DIFFRACTION98
1.7042-1.72760.21811410.20051965X-RAY DIFFRACTION96
1.7276-1.75230.25631410.19471995X-RAY DIFFRACTION97
1.7523-1.77840.24151210.19351937X-RAY DIFFRACTION98
1.7784-1.80620.26471470.19551918X-RAY DIFFRACTION96
1.8062-1.83580.26881510.20312004X-RAY DIFFRACTION98
1.8358-1.86750.27411200.20661916X-RAY DIFFRACTION96
1.8675-1.90140.21821420.19171960X-RAY DIFFRACTION98
1.9014-1.9380.23171300.18841999X-RAY DIFFRACTION97
1.938-1.97760.25041120.18831948X-RAY DIFFRACTION97
1.9776-2.02060.20521740.18741953X-RAY DIFFRACTION97
2.0206-2.06760.22681390.18181962X-RAY DIFFRACTION98
2.0676-2.11930.18941380.18091992X-RAY DIFFRACTION97
2.1193-2.17660.21091390.17132023X-RAY DIFFRACTION99
2.1766-2.24060.2141300.1781911X-RAY DIFFRACTION98
2.2406-2.3130.18891480.17912055X-RAY DIFFRACTION99
2.313-2.39560.19031350.18021922X-RAY DIFFRACTION99
2.3956-2.49150.24881480.19092029X-RAY DIFFRACTION99
2.4915-2.60490.23721450.18662032X-RAY DIFFRACTION99
2.6049-2.74220.20911270.19431988X-RAY DIFFRACTION100
2.7422-2.9140.23751480.18961996X-RAY DIFFRACTION100
2.914-3.1390.20481430.17862019X-RAY DIFFRACTION100
3.139-3.45480.22331470.17992049X-RAY DIFFRACTION100
3.4548-3.95450.20221400.17591993X-RAY DIFFRACTION100
3.9545-4.98140.191430.15682007X-RAY DIFFRACTION100
4.9814-47.39730.20281500.17382018X-RAY DIFFRACTION100

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