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- PDB-5wv4: X-ray Crystal Structure of Pseudoazurin Met16Gly variant -

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Basic information

Entry
Database: PDB / ID: 5wv4
TitleX-ray Crystal Structure of Pseudoazurin Met16Gly variant
ComponentsPseudoazurin
KeywordsELECTRON TRANSPORT / Electron Transfer
Function / homology
Function and homology information


electron transfer activity / periplasmic space / 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 / molecular replacement / Resolution: 1.8 Å
AuthorsTamaoki, S. / Yamaguchi, T. / Kohzuma, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science22550145 Japan
CitationJournal: To Be Published
Title: X-ray Crystal Structure of Pseudoazurin Met16Gly variant
Authors: Tamaoki, S. / Yamaguchi, T. / Kohzuma, T.
History
DepositionDec 22, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: 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

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Assembly

Deposited unit
A: Pseudoazurin
B: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0454
Polymers25,9182
Non-polymers1272
Water3,999222
1
A: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0222
Polymers12,9591
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0222
Polymers12,9591
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.236, 93.857, 34.628
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-373-

HOH

21A-390-

HOH

31A-433-

HOH

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Components

#1: Protein Pseudoazurin / Blue copper protein


Mass: 12958.796 Da / Num. of mol.: 2 / Mutation: M16G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter cycloclastes (bacteria) / Gene: bcp / Production host: Escherichia coli (E. coli) / References: UniProt: P19567
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


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


Mass: 18.015 Da / Num. of mol.: 222 / 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: 1.89 Å3/Da / Density % sol: 34.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 28% PEG 4000, 0.1 M Tris-HCl buffer

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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 270 / Detector: CCD / Date: Jun 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 19052 / % possible obs: 99.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.8-1.8370.480.9091100
1.83-1.866.90.4690.8871100
1.86-1.970.4130.9171100
1.9-1.9470.3530.9391100
1.94-1.986.90.3140.9491100
1.98-2.0370.2840.9541100
2.03-2.0870.2470.961100
2.08-2.1370.2260.9691100
2.13-2.270.2050.9711100
2.2-2.277.10.2010.9751100
2.27-2.357.10.1860.9761100
2.35-2.447.10.1670.9761100
2.44-2.557.10.1590.9841100
2.55-2.697.10.1360.9881100
2.69-2.867.10.1230.991100
2.86-3.0870.1150.9911100
3.08-3.3970.0970.9941100
3.39-3.886.70.0860.994198.8
3.88-4.886.50.0730.994197.8
4.88-506.10.0720.991197.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.79 Å30.02 Å
Translation1.79 Å30.02 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
SCALEPACKdata scaling
MOLREP10.2.35phasing
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BQK

1bqk


Resolution: 1.8→30.02 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.873 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.154
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2416 957 5.1 %RANDOM
Rwork0.1795 ---
obs0.1826 17765 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 63.76 Å2 / Biso mean: 25.246 Å2 / Biso min: 4.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0 Å2
2---0.07 Å20 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 1.8→30.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1818 0 2 237 2057
Biso mean--18.04 30.98 -
Num. residues----248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191951
X-RAY DIFFRACTIONr_bond_other_d0.0020.021902
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.972645
X-RAY DIFFRACTIONr_angle_other_deg0.92134424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1235265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01726.48674
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58715336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.226152
X-RAY DIFFRACTIONr_chiral_restr0.0890.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212271
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02391
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 76 -
Rwork0.238 1270 -
all-1346 -
obs--99.41 %
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)
11.20930.4327-0.79471.7055-0.79480.84060.03470.00560.0983-0.03290.03540.06060.05530.0254-0.07010.0847-0.01840.00670.1125-0.00620.00916.86769.977217.3408
22.1197-0.48990.30360.6555-1.09722.00010.10440.0760.0004-0.09660.10.14320.1463-0.1189-0.20430.0499-0.0564-0.08810.090.11490.165610.414432.652833.0915
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 124
2X-RAY DIFFRACTION2B1 - 124

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