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- PDB-8k9p: Neutron X-ray joint structure of pseudoazurin from Alcaligenes fa... -

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Basic information

Entry
Database: PDB / ID: 8k9p
TitleNeutron X-ray joint structure of pseudoazurin from Alcaligenes faecalis
ComponentsPseudoazurin
KeywordsELECTRON TRANSPORT / blue copper / electron transfer
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. / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / DEUTERATED WATER / Pseudoazurin
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFukuda, Y. / Kurihara, K. / Inoue, T. / Tamada, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Biochemistry / Year: 2024
Title: Overlooked Hydrogen Bond in a Blue Copper Protein Uncovered by Neutron and Sub- angstrom ngstrom Resolution X-ray Crystallography.
Authors: Fukuda, Y. / Lintuluoto, M. / Kurihara, K. / Hasegawa, K. / Inoue, T. / Tamada, T.
History
DepositionAug 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)13,8323
Polymers13,6731
Non-polymers1602
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-6 kcal/mol
Surface area7270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.168, 50.168, 98.292
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Pseudoazurin / Blue copper protein / Cupredoxin


Mass: 13672.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04377
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: D2O
Has ligand of interestY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.8 M deuterated ammonium sulfate

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Data collection

Diffraction
IDMean temperature (K)Ambient temp detailsCrystal-IDSerial crystal experiment
1293room temperature1N
2293room temperature1N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
NUCLEAR REACTORJRR-3M 1G-A22.9
Detector
TypeIDDetectorDate
LADI III1IMAGE PLATEJul 19, 2022
DECTRIS PILATUS3 S 6M2PIXELOct 20, 2022
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMneutron2Si(111)
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.91
Reflection

Biso Wilson estimate: 18.25 Å2 / Entry-ID: 8K9P

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)
1.3-49.153442510010.10.9980.0710.023116.9
1.9-1009935902.80.9880.1080.07426.99
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allDiffraction-ID% possible all
1.3-1.329.10.8952.417070.8080.31199.4
1.9-1.971.80.3962.099140.6020.355283.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
Refinement

SU ML: 0.1168 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 17.3164 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)
1.5-43.45X-RAY DIFFRACTION450.16920.12880.1332272201502242210.1310011.38
1.9-39.7NEUTRON DIFFRACTION0.2770.213992190.042
Refinement stepCycle: LAST / Resolution: 1.5→43.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms938 0 6 72 1016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00932156
X-RAY DIFFRACTIONf_angle_d1.21293784
X-RAY DIFFRACTIONf_chiral_restr0.0678164
X-RAY DIFFRACTIONf_plane_restr0.0091345
X-RAY DIFFRACTIONf_dihedral_angle_d18.7808537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.18551360.12771275X-RAY DIFFRACTION100
1.53-1.570.15511370.11911255X-RAY DIFFRACTION100
1.57-1.610.18511390.11711261X-RAY DIFFRACTION100
1.61-1.650.19041450.12521238X-RAY DIFFRACTION100
1.65-1.70.21911400.15471261X-RAY DIFFRACTION100
1.7-1.750.21061370.14351249X-RAY DIFFRACTION100
1.75-1.820.14111400.12171267X-RAY DIFFRACTION100
1.82-1.890.14091420.12151259X-RAY DIFFRACTION99.93
1.89-1.980.18241450.11731258X-RAY DIFFRACTION100
1.98-2.080.16841460.13011259X-RAY DIFFRACTION100
2.08-2.210.17241480.12941252X-RAY DIFFRACTION100
2.21-2.380.16381410.13011264X-RAY DIFFRACTION100
2.38-2.620.18861410.13691255X-RAY DIFFRACTION100
2.62-30.18881400.15261260X-RAY DIFFRACTION100
3-3.770.18521410.12791265X-RAY DIFFRACTION100
3.78-43.450.14011540.11661272X-RAY DIFFRACTION100

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