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- PDB-5yw3: X-ray Crystal Structure of Pseudoazurin Thr36Lys Variant -

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Basic information

Entry
Database: PDB / ID: 5yw3
TitleX-ray Crystal Structure of Pseudoazurin Thr36Lys Variant
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.19 Å
AuthorsSakai, C. / 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 Thr36Lys Variant
Authors: Yamaguchi, T. / Sakai, C. / Kohzuma, T.
History
DepositionNov 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 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
C: Pseudoazurin
D: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,60511
Polymers52,2444
Non-polymers3617
Water15,043835
1
A: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1252
Polymers13,0611
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6240 Å2
MethodPISA
2
B: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1603
Polymers13,0611
Non-polymers992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6450 Å2
MethodPISA
3
C: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1603
Polymers13,0611
Non-polymers992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6280 Å2
MethodPISA
4
D: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1603
Polymers13,0611
Non-polymers992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-7 kcal/mol
Surface area6420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.699, 51.227, 57.723
Angle α, β, γ (deg.)88.88, 77.16, 86.58
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Pseudoazurin / Blue copper protein


Mass: 13061.016 Da / Num. of mol.: 4 / Mutation: 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


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 835 / 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: 1.91 Å3/Da / Density % sol: 35.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100mM Tris-HCl, 38% PEG4000, 40mg/mL protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.19→50 Å / Num. obs: 117085 / % possible obs: 94.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.077 / Χ2: 0.975 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.19-1.213.60.34255380.542189.7
1.21-1.233.90.35157190.623191.1
1.23-1.2640.32656420.638191.4
1.26-1.2840.29357240.665191.7
1.28-1.3140.26457320.679192.1
1.31-1.3440.2457410.703192.3
1.34-1.3740.22157620.736192.8
1.37-1.4140.19357960.706193.2
1.41-1.4540.18158120.787193.5
1.45-1.540.1558370.78193.9
1.5-1.5540.12858810.806194.2
1.55-1.6240.11358550.838194.7
1.62-1.6940.10459120.87195.1
1.69-1.7840.08959550.926195.6
1.78-1.8940.07459551.009195.8
1.89-2.0340.06559981.18196.4
2.03-2.2440.05960391.321196.8
2.24-2.563.90.05860281.454197.4
2.56-3.233.90.05361131.57197.8
3.23-503.80.05760462.53197.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BQK

1bqk


Resolution: 1.19→24.72 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.494 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17297 5906 5 %RANDOM
Rwork0.12657 ---
obs0.12886 111149 93.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.281 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0.02 Å20.1 Å2
2--0.04 Å20.04 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.19→24.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3660 0 7 835 4502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0194023
X-RAY DIFFRACTIONr_bond_other_d0.0020.023881
X-RAY DIFFRACTIONr_angle_refined_deg2.5331.9775442
X-RAY DIFFRACTIONr_angle_other_deg1.1923.0019103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0455549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7626.389144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27615718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.432154
X-RAY DIFFRACTIONr_chiral_restr0.1690.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214595
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02709
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_it1.6270.8282124
X-RAY DIFFRACTIONr_mcbond_other1.6280.8282123
X-RAY DIFFRACTIONr_mcangle_it1.8881.252697
X-RAY DIFFRACTIONr_mcangle_other1.8881.252698
X-RAY DIFFRACTIONr_scbond_it2.3861.0431899
X-RAY DIFFRACTIONr_scbond_other2.3861.0431896
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7811.462744
X-RAY DIFFRACTIONr_long_range_B_refined3.93813.0244726
X-RAY DIFFRACTIONr_long_range_B_other3.77112.6494647
X-RAY DIFFRACTIONr_rigid_bond_restr4.94337904
X-RAY DIFFRACTIONr_sphericity_free18.8435528
X-RAY DIFFRACTIONr_sphericity_bonded7.81858266
LS refinement shellResolution: 1.188→1.219 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 463 -
Rwork0.261 7545 -
obs--87.32 %
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)
10.0121-0.0041-0.00530.04160.0070.0263-0.0004-0.00110.00010.0018-0.00070.00280.00150.00050.00110.00090.0003-0.00140.0006-0.00080.00320.01930.89670.5636
20.02670.00550.00730.0174-0.00030.02280.00060.00060-0.0009-0.0007-0.0003-0.0004-0.00050.00010.00080.0006-0.00140.001-0.00110.00317.016326.33822.3923
30.03270.007-0.01220.0160.0140.04990.00020.0010.00090.0002-0.0007-0.0003-0.0006-0.00010.00050.00090.0005-0.00170.0008-0.00090.003419.574941.636527.1666
40.0088-0.00230.00080.0135-0.00070.04530.0003-0.0010.0003-0.00030.00080.00030.00080.001-0.00110.00110.0003-0.0020.0002-0.00060.003814.755516.542832.2754
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 503
2X-RAY DIFFRACTION2B1 - 492
3X-RAY DIFFRACTION3C1 - 508
4X-RAY DIFFRACTION4D1 - 531

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