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- PDB-3l45: A Joint Neutron and X-ray structure of Oxidized Amicyanin -

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Basic information

Entry
Database: PDB / ID: 3l45
TitleA Joint Neutron and X-ray structure of Oxidized Amicyanin
ComponentsAmicyanin
KeywordsELECTRON TRANSPORT / Type-I Blue Copper Protein / Beta Sandwich / Metal-binding
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Amicyanin, Paracoccus/Methylobacterium / Amicyanin / 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 ...Amicyanin, Paracoccus/Methylobacterium / Amicyanin / 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 / DEUTERATED WATER / Amicyanin
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSukumar, N. / Mathews, F.S. / Langan, P. / Davidson, V.L.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: A joint x-ray and neutron study on amicyanin reveals the role of protein dynamics in electron transfer.
Authors: Sukumar, N. / Mathews, F.S. / Langan, P. / Davidson, V.L.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: A preliminary time-of-flight neutron diffraction study on amicyanin from Paracoccus denitrificans
Authors: Sukumar, N. / Langan, P. / Mathews, F.S. / Jones, L.H. / Thiyagarajan, P. / Schoenborn, B.P. / Davidson, V.L.
History
DepositionDec 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Data collection / Version format compliance
Revision 1.2Apr 25, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 1.3Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Amicyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5692
Polymers11,5051
Non-polymers641
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.540, 56.580, 28.860
Angle α, β, γ (deg.)90.00, 96.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Amicyanin


Mass: 11505.171 Da / Num. of mol.: 1 / Fragment: UNP residues 27-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Gene: ami, mauC / Production host: Escherichia coli (E. coli) / References: UniProt: P22364
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
NEUTRON DIFFRACTION1
X-RAY DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.76 %
Crystal growTemperature: 291 K
Details: 2.4M ammonium sulfate, 100mM citric acid pH5 and 3M sodium monobasic/potassium dibasic phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.98
NUCLEAR REACTORLANSCE PCS21.1-5
Detector
TypeIDDetectorDetails
ADSC QUANTUM 3151CCDMIRRORS
IMAGE PLATE2TOF AREA DETECTOR
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SISINGLE WAVELENGTHMx-ray1
2LAUELneutron1
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
21.11
351
ReflectionResolution: 1.8→28 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.256 / Net I/σ(I): 4.2
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1635

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Processing

Software
NameVersionClassificationNB
nCNS1.0.0refinement
HKL-2000data reduction
d*TREKdata reduction
HKL-2000data scaling
LAUENORMdata scaling
SCALAdata scaling
EPMRphasing
Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Starting model: PDB ENTRY 1AAC

1aac

/ Stereochemistry target values: JOINT X-RAY/NEUTRON ML

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection obs% reflection Rfree (%)R Free selection detailsDiffraction-IDIsotropic thermal modelCross valid methodSolvent model% reflection obs (%)
1.8-28NEUTRON DIFFRACTION0.2340.2090.20960784.8RANDOM2ISOTROPICTHROUGHTOUTCNS BULK SOLVENT MODEL USED
1.5-50X-RAY DIFFRACTION0.2150.19811364195.4
Refine analyzeLuzzati d res high obs: 1.8
Refinement stepCycle: LAST / Resolution: 1.8→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms807 0 1 91 899
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONc_bond_d0.021
NEUTRON DIFFRACTIONc_bond_d_na
NEUTRON DIFFRACTIONc_bond_d_prot
NEUTRON DIFFRACTIONc_angle_d
NEUTRON DIFFRACTIONc_angle_d_na
NEUTRON DIFFRACTIONc_angle_d_prot
NEUTRON DIFFRACTIONc_angle_deg2
NEUTRON DIFFRACTIONc_angle_deg_na
NEUTRON DIFFRACTIONc_angle_deg_prot
NEUTRON DIFFRACTIONc_dihedral_angle_d17.6
NEUTRON DIFFRACTIONc_dihedral_angle_d_na
NEUTRON DIFFRACTIONc_dihedral_angle_d_prot
NEUTRON DIFFRACTIONc_improper_angle_d1.65
NEUTRON DIFFRACTIONc_improper_angle_d_na
NEUTRON DIFFRACTIONc_improper_angle_d_prot
NEUTRON DIFFRACTIONc_mcbond_it
NEUTRON DIFFRACTIONc_mcangle_it
NEUTRON DIFFRACTIONc_scbond_it
NEUTRON DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.5→1.55 Å / % reflection obs: 96.5 %

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