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- PDB-5y23: X-ray crystal structure of Pseudoazurin Met16Phe variant -

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Basic information

Entry
Database: PDB / ID: 5y23
TitleX-ray crystal structure of Pseudoazurin Met16Phe variant
ComponentsPseudoazurin
KeywordsELECTRON TRANSPORT / Electron transfer / Cupredoxin
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Pseudoazurin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / 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 ...Pseudoazurin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / 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 / Pseudoazurin
Similarity search - Component
Biological speciesAchromobacter cycloclastes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsYamaguchi, T. / Akao, K. / Kohzuma, T.
CitationJournal: To Be Published
Title: X-ray crystal structure of Pseudoazurin Met16Phe variant
Authors: Yamaguchi, T. / Akao, K. / Kohzuma, T.
History
DepositionJul 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pseudoazurin
B: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,77710
Polymers26,0982
Non-polymers6808
Water5,729318
1
A: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3895
Polymers13,0491
Non-polymers3404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-0 kcal/mol
Surface area6320 Å2
MethodPISA
2
B: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3895
Polymers13,0491
Non-polymers3404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-1 kcal/mol
Surface area6040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.715, 59.620, 54.324
Angle α, β, γ (deg.)90.000, 105.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pseudoazurin / Blue copper protein


Mass: 13048.918 Da / Num. of mol.: 2 / Mutation: M16F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter cycloclastes (bacteria) / Gene: bcp / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P19567
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Drop: 100 mM Tris-HCl buffer, 15.5 % PEG4000, 31 mg/mL Protein Reservoir: 100 mM Tris-HCl buffer, 31 % PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 40971 / % possible obs: 97.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.058 / Χ2: 0.999 / Net I/σ(I): 9.8 / Num. measured all: 154641
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
1.4-1.453.70.2310.507196
1.45-1.513.80.1740.552196.5
1.51-1.583.80.140.598197
1.58-1.663.80.110.635197.3
1.66-1.763.80.0930.71197.7
1.76-1.93.80.0740.877198.1
1.9-2.093.80.0611.12198.5
2.09-2.393.80.0551.303199
2.39-3.023.80.0481.502199.3
3.02-503.60.0472.223194.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BQK

1bqk


Resolution: 1.4→26.2 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.707 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.064
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1816 2069 5.1 %RANDOM
Rwork0.141 ---
obs0.143 38882 97.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.3 Å2 / Biso mean: 15.307 Å2 / Biso min: 4.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å2-0.15 Å2
2--0.25 Å20 Å2
3---0.18 Å2
Refinement stepCycle: final / Resolution: 1.4→26.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 50 353 2235
Biso mean--27.92 28.14 -
Num. residues----248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0192039
X-RAY DIFFRACTIONr_bond_other_d0.0020.022028
X-RAY DIFFRACTIONr_angle_refined_deg2.6431.9892762
X-RAY DIFFRACTIONr_angle_other_deg1.13934721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7955278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89426.16473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.47915353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.793152
X-RAY DIFFRACTIONr_chiral_restr0.1520.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212330
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02408
LS refinement shellResolution: 1.4→1.437 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 164 -
Rwork0.184 2802 -
all-2966 -
obs--94.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.19540.36040.13381.15390.17340.7485-0.02260.0482-0.0248-0.02930.0255-0.0331-0.01790.03-0.00290.0614-0.00670.00970.0038-0.0010.00411.90680.309721.846
21.88630.08050.09930.43420.06970.76190.0574-0.07190.02080.0245-0.0518-0.0319-0.0086-0.0071-0.00550.0435-0.00640.010.0170.00760.008828.02682.1242-2.4259
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 124
2X-RAY DIFFRACTION2B1 - 124

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