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- PDB-5xmo: X-ray crystal structure of Pseudoazurin Met16Phe/Thr36Lys variant -

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Basic information

Entry
Database: PDB / ID: 5xmo
TitleX-ray crystal structure of Pseudoazurin Met16Phe/Thr36Lys variant
ComponentsPseudoazurin
KeywordsELECTRON TRANSPORT / Electron transfer / Cupredoxin
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: 1.19 Å
AuthorsYamaguchi, T. / Kohzuma, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science22550145 Japan
CitationJournal: Photon Factory Activity Report / Year: 2017
Title: X-ray Crystallographic Analysis of M16F/T36K Double Mutant of Pseudoazurin
Authors: Yamaguchi, T. / Takebayashi, N. / Akao, K. / Sakai, C. / Kohzuma, T.
History
DepositionMay 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1412
Polymers13,0771
Non-polymers641
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6380 Å2
Unit cell
Length a, b, c (Å)93.170, 41.160, 34.830
Angle α, β, γ (deg.)90.00, 98.71, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-306-

HOH

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Components

#1: Protein Pseudoazurin / Blue copper protein


Mass: 13076.994 Da / Num. of mol.: 1 / Mutation: M16F, T36K
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.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Buffer for crystallization: 0.1 M sodium acetate pH 4.5 Precipitant: 30 % PEG1500 Soaking (Cryoprotectant): 0.1 M Tris-HCl pH 7.5, 40 % PEG1500

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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 210 / Detector: CCD / Date: May 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.192→46.048 Å / Num. obs: 38384 / % possible obs: 92.3 % / Redundancy: 5.4 % / Rpim(I) all: 0.033 / Rrim(I) all: 0.079 / Rsym value: 0.072 / Net I/av σ(I): 6.8 / Net I/σ(I): 12.5
Reflection shellResolution: 1.192→1.223 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 4.4 / % possible all: 87.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.517
Highest resolutionLowest resolution
Rotation24.61 Å1.33 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALA3.3.22data scaling
iMOSFLM7.2.1data processing
PDB_EXTRACT3.22data extraction
MOLREP11.4.06phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BQK

1bqk


Resolution: 1.19→46.05 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.157 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16116 1936 5 %RANDOM
Rwork0.12792 ---
obs0.12965 36446 92.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.494 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20 Å2
2---0 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.19→46.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms918 0 1 208 1127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0191020
X-RAY DIFFRACTIONr_bond_other_d0.0040.02981
X-RAY DIFFRACTIONr_angle_refined_deg2.7711.9731387
X-RAY DIFFRACTIONr_angle_other_deg1.25632303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9645141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.74526.21637
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.69415183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.716151
X-RAY DIFFRACTIONr_chiral_restr0.1920.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211184
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02185
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4930.956540
X-RAY DIFFRACTIONr_mcbond_other1.4350.954539
X-RAY DIFFRACTIONr_mcangle_it1.8641.444689
X-RAY DIFFRACTIONr_mcangle_other1.9031.446690
X-RAY DIFFRACTIONr_scbond_it2.961.28480
X-RAY DIFFRACTIONr_scbond_other2.9651.276477
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1581.774697
X-RAY DIFFRACTIONr_long_range_B_refined4.6915.1181205
X-RAY DIFFRACTIONr_long_range_B_other3.20113.2491136
X-RAY DIFFRACTIONr_rigid_bond_restr5.94232001
X-RAY DIFFRACTIONr_sphericity_free30.9955142
X-RAY DIFFRACTIONr_sphericity_bonded9.29652077
LS refinement shellResolution: 1.192→1.223 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 148 -
Rwork0.193 2534 -
obs--87.3 %

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