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- PDB-3ef4: Crystal structure of native pseudoazurin from Hyphomicrobium deni... -

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Basic information

Entry
Database: PDB / ID: 3ef4
TitleCrystal structure of native pseudoazurin from Hyphomicrobium denitrificans
ComponentsBlue copper protein
KeywordsELECTRON TRANSPORT / copper / electron transfer / blue copper protein
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 / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / PHOSPHATE ION / Pseudoazurin
Similarity search - Component
Biological speciesHyphomicrobium denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsHira, D. / Nojiri, M. / Suzuki, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Atomic resolution structure of pseudoazurin from the methylotrophic denitrifying bacterium Hyphomicrobium denitrificans: structural insights into its spectroscopic properties
Authors: Hira, D. / Nojiri, M. / Suzuki, S.
History
DepositionSep 8, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Blue copper protein
B: Blue copper protein
C: Blue copper protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,38721
Polymers40,7723
Non-polymers1,61518
Water9,008500
1
A: Blue copper protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0346
Polymers13,5911
Non-polymers4435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Blue copper protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2248
Polymers13,5911
Non-polymers6337
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Blue copper protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1297
Polymers13,5911
Non-polymers5386
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.690, 50.623, 82.378
Angle α, β, γ (deg.)90.00, 90.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-520-

HOH

21C-579-

HOH

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Components

#1: Protein Blue copper protein / pseudoazurin


Mass: 13590.666 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Hyphomicrobium denitrificans (bacteria) / References: UniProt: A7VL37
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 3.2M Ammonium Phosphate, 0.05M Potassium Phosphate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jun 13, 2006
RadiationMonochromator: double Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.18→49.2 Å / Num. all: 132934 / Num. obs: 132934 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 43.59
Reflection shellResolution: 1.18→1.22 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.78 / % possible all: 85.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPREFMAC SHELXphasing
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1adw

1adw


Resolution: 1.18→44.95 Å / Num. parameters: 32026 / Num. restraintsaints: 45026 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.169 6376 5.27 %RANDOM
Rwork0.135 ---
obs0.135 121025 95.8 %-
all-132934 --
Refine analyzeNum. disordered residues: 30 / Occupancy sum hydrogen: 2724 / Occupancy sum non hydrogen: 3402
Refinement stepCycle: LAST / Resolution: 1.18→44.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2879 0 83 519 3481
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.033

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