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- PDB-5ysg: X-ray Crystal Structure of Pseudoazurin Met16Gly Variant, Reduced... -

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Basic information

Entry
Database: PDB / ID: 5ysg
TitleX-ray Crystal Structure of Pseudoazurin Met16Gly Variant, Reduced Form.
ComponentsPseudoazurin
KeywordsELECTRON TRANSPORT / ELECTRON TRNASPORT
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsKohei, A. / 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, Reduced Form.
Authors: Kohei, A. / Yamaguchi, T. / Kohzuma, T.
History
DepositionNov 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 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

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Assembly

Deposited unit
A: Pseudoazurin
B: Pseudoazurin
C: Pseudoazurin
D: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,73415
Polymers51,8354
Non-polymers89911
Water7,476415
1
A: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2074
Polymers12,9591
Non-polymers2483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-1 kcal/mol
Surface area5960 Å2
MethodPISA
2
B: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2074
Polymers12,9591
Non-polymers2483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-1 kcal/mol
Surface area5970 Å2
MethodPISA
3
C: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2074
Polymers12,9591
Non-polymers2483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-0 kcal/mol
Surface area5990 Å2
MethodPISA
4
D: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1143
Polymers12,9591
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-1 kcal/mol
Surface area5950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.530, 91.490, 78.570
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Pseudoazurin / Blue copper protein


Mass: 12958.796 Da / Num. of mol.: 4 / 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


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 3.17 Å3/Da / Density % sol: 61.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 30 % PEG1000, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jun 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→30.002 Å / Num. obs: 43773 / % possible obs: 100 % / Redundancy: 3.6 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.065 / Rsym value: 0.055 / Net I/av σ(I): 12.2 / Net I/σ(I): 15.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2-2.113.50.3522.263670.220.4170.352100
2.11-2.243.50.25360230.1560.2960.25100
2.24-2.393.60.1894.156460.1180.2230.189100
2.39-2.583.60.1266.153140.0780.1480.126100
2.58-2.833.60.0849.248500.0520.0990.084100
2.83-3.163.70.06112.344130.0370.0710.061100
3.16-3.653.70.04216.938930.0250.0490.042100
3.65-4.473.70.02525.932840.0150.0290.025100
4.47-6.323.70.02227.725680.0140.0260.022100
6.32-29.9223.50.02323.514150.0150.0270.02399.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.599
Highest resolutionLowest resolution
Rotation29.91 Å2.32 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALA3.3.22data scaling
MOLREPphasing
PDB_EXTRACT3.22data extraction
Cootmodel building
CrystalCleardata collection
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BQK

1bqk


Resolution: 2→29.92 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.345 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20254 2191 5 %RANDOM
Rwork0.17209 ---
obs0.17369 41565 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.023 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3531 0 46 415 3992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193690
X-RAY DIFFRACTIONr_bond_other_d0.0030.023620
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.9754981
X-RAY DIFFRACTIONr_angle_other_deg1.06738386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8885483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48926.176136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67515611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.16154
X-RAY DIFFRACTIONr_chiral_restr0.1270.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214165
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02735
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_it2.9892.7491938
X-RAY DIFFRACTIONr_mcbond_other2.9842.7481937
X-RAY DIFFRACTIONr_mcangle_it3.9694.0882419
X-RAY DIFFRACTIONr_mcangle_other3.974.0892420
X-RAY DIFFRACTIONr_scbond_it4.2063.1751752
X-RAY DIFFRACTIONr_scbond_other4.2043.1751752
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3614.5212563
X-RAY DIFFRACTIONr_long_range_B_refined8.72223.1454071
X-RAY DIFFRACTIONr_long_range_B_other8.53522.6353933
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 158 -
Rwork0.217 3072 -
obs--100 %

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