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- PDB-5ai2: Anomalous Neutron phased crystal structure of 113Cd-substituted P... -

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Basic information

Entry
Database: PDB / ID: 5ai2
TitleAnomalous Neutron phased crystal structure of 113Cd-substituted Perdeuterated Pyrococcus furiosus rubredoxin to 1.75A resolution at 295K
ComponentsRUBREDOXIN
KeywordsELECTRON TRANSPORT / NEUTRON ANOMALOUS PHASING / PERDEUTERATED / PYROCOCCUS FURIOSUS / RUBREDOXIN / CADMIUM
Function / homology
Function and homology information


alkane catabolic process / electron transfer activity / iron ion binding
Similarity search - Function
Rubredoxin / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / Single Sheet / Mainly Beta
Similarity search - Domain/homology
: / : / DEUTERATED WATER / Rubredoxin
Similarity search - Component
Biological speciesPYROCOCCUS FURIOSUS (archaea)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / EXPERIMENTAL ANOMALOUS NEUTRON PHASING / Resolution: 1.75 Å
AuthorsCuypers, M.G. / Mossou, E. / Mason, S.A.
CitationJournal: Sci.Rep. / Year: 2016
Title: Macromolecular Structure Phasing by Neutron Anomalous Diffraction.
Authors: Cuypers, M.G. / Mason, S.A. / Mossou, E. / Haertlein, M. / Forsyth, V.T. / Mitchell, E.P.
History
DepositionFeb 11, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Atomic model / Non-polymer description / Other
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: RUBREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1505
Polymers6,0321
Non-polymers1184
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.440, 34.140, 43.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RUBREDOXIN


Mass: 6031.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: PERDEUTERATED, 113-CD SUBSTITUTED, CARBOXYLIC DEUTERONS
Source: (natural) PYROCOCCUS FURIOSUS (archaea) / References: UniProt: P24297
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-D8U / deuterium(1+)


Mass: 2.014 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: D
#4: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: D2O
Nonpolymer detailsCADMIUM ION (CD): MINIMUM 95 PERCENT PURE 113-CD ISOTOPE IN CRYSTAL. TRACE AMOUNTS OF FE ONLY ...CADMIUM ION (CD): MINIMUM 95 PERCENT PURE 113-CD ISOTOPE IN CRYSTAL. TRACE AMOUNTS OF FE ONLY DETECTED BY CRYSTAL X-RAY FLUORESCENCE.

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.35 % / Description: RPIM GIVEN INSTEAD OF RSYM
Crystal growpH: 6.5 / Details: PH 6.5

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: ILL / Beamline: D19 / Type: ILL / Wavelength: 1.17
DetectorType: INSTITUT LAUE LANGEVIN DETECTOR GROUP / Detector: 5ATM 3HE, CURVED 120X30 DEGREES / Date: Dec 1, 2014 / Details: BORON CARBIDE BEAM DEFINING APERTURE
RadiationScattering type: neutron
Radiation wavelengthWavelength: 1.17 Å / Relative weight: 1
ReflectionResolution: 1.75→34.44 Å / Num. obs: 5560 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 13.4 % / Biso Wilson estimate: 8.7 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.04
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 5.4 / Rsym value: 0.149 / % possible all: 99.9

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Processing

Software
NameClassification
PHENIXrefinement
SHELXCDphasing
SHELXEphasing
RETREATdata reduction
RETREATdata scaling
RefinementMethod to determine structure: EXPERIMENTAL ANOMALOUS NEUTRON PHASING
Starting model: NONE

Resolution: 1.75→27.068 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 30.24 / Stereochemistry target values: ML
Details: USED NEUTRON BOUND COHERENT SCATTERING LENGTH FOR 113-CD OF -8.0 FM FOR REFINEMENT
RfactorNum. reflection% reflection
Rfree0.2864 451 4.5 %
Rwork0.2331 --
obs0.2357 10050 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→27.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms421 0 1 48 470
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.003992
NEUTRON DIFFRACTIONf_angle_d0.6131766
NEUTRON DIFFRACTIONf_dihedral_angle_d14.246258
NEUTRON DIFFRACTIONf_chiral_restr0.02463
NEUTRON DIFFRACTIONf_plane_restr0.002184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-2.00320.27651560.21543215NEUTRON DIFFRACTION100
2.0032-2.52360.25521160.22163230NEUTRON DIFFRACTION100
2.5236-27.07160.30471790.2493154NEUTRON DIFFRACTION100

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