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- PDB-3pni: Crystal structure of D14C [3Fe-4S] Pyrococcus furiosus ferredoxin -

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Basic information

Entry
Database: PDB / ID: 3pni
TitleCrystal structure of D14C [3Fe-4S] Pyrococcus furiosus ferredoxin
ComponentsFerredoxin
KeywordsELECTRON TRANSPORT / ferredoxin / iron-sulfur cluster / pyrococcus furiosus / two molecules in asymmetric unit / Metal-binding
Function / homology
Function and homology information


3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding
Similarity search - Function
4Fe-4S single cluster domain of Ferredoxin I / 3Fe-4S ferredoxin / Alpha-Beta Plaits - #20 / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / FE3-S4 CLUSTER / Ferredoxin
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLoevgreen, M.N. / Christensen, H.E.M. / Harris, P.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2011
Title: Crystal structures of the all cysteinyl coordinated D14C variant of Pyrococcus furiosus ferredoxin: [4Fe-4S] <-> [3Fe-4S] cluster conversion
Authors: Lovgreen, M.N. / Martic, M. / Windahl, M.S. / Christensen, H.E. / Harris, P.
History
DepositionNov 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _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: Ferredoxin
B: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1458
Polymers14,3182
Non-polymers8276
Water0
1
A: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5143
Polymers7,1591
Non-polymers3552
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6325
Polymers7,1591
Non-polymers4734
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Ferredoxin
hetero molecules

A: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1458
Polymers14,3182
Non-polymers8276
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area1670 Å2
ΔGint-67 kcal/mol
Surface area7330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.400, 49.800, 51.230
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 Ferredoxin /


Mass: 7159.056 Da / Num. of mol.: 2 / Fragment: Ferredoxin / Mutation: D14C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM3638 / Gene: fdxA, PF1909 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3) / References: UniProt: P29603
#2: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co

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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: 2.11 Å3/Da / Density % sol: 41.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 35% PEG1500, 100mM Tris/HCl, 10mM [Co(NH3)6]Cl3, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2010
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.8→35.7 Å / Num. all: 3254 / Num. obs: 3087 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.5 % / Num. unique all: 456 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z8Q

2z8q


Resolution: 2.8→35.7 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.86 / SU B: 22.577 / SU ML: 0.426 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.52 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31849 141 4.4 %RANDOM
Rwork0.27892 ---
obs0.28053 3087 99.75 %-
all-3254 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.344 Å2
Baniso -1Baniso -2Baniso -3
1--5.8 Å20 Å20 Å2
2--10.16 Å20 Å2
3----4.36 Å2
Refinement stepCycle: LAST / Resolution: 2.8→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 0 18 0 1006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221039
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5112.0261454
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2025134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.01728.63644
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.72315178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021766
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4271.5671
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8621085
X-RAY DIFFRACTIONr_scbond_it1.3933368
X-RAY DIFFRACTIONr_scangle_it2.34.5314
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 6 -
Rwork0.38 221 -
obs--100 %

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