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- PDB-3wcq: Crystal structure analysis of Cyanidioschyzon melorae ferredoxin ... -

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Basic information

Entry
Database: PDB / ID: 3wcq
TitleCrystal structure analysis of Cyanidioschyzon melorae ferredoxin D58N mutant
ComponentsFerredoxin
KeywordsELECTRON TRANSPORT / 2Fe-2S cluster / electron transfer / FNR
Function / homology
Function and homology information


chloroplast / electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) ...Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Ferredoxin
Similarity search - Component
Biological speciesCyanidioschyzon merolae (eukaryote)
MethodX-RAY DIFFRACTION / SAD / Resolution: 0.97 Å
AuthorsUeno, Y. / Matsumoto, T. / Yamano, A. / Imai, T. / Morimoto, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Increasing the electron-transfer ability of Cyanidioschyzon merolae ferredoxin by a one-point mutation - A high resolution and Fe-SAD phasing crystal structure analysis of the Asp58Asn mutant
Authors: Ueno, Y. / Matsumoto, T. / Yamano, A. / Imai, T. / Morimoto, Y.
History
DepositionMay 31, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_seq_id / _struct_conn.ptnr1_label_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7562
Polymers10,5801
Non-polymers1761
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.026, 46.527, 66.139
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: 10579.804 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanidioschyzon merolae (eukaryote) / Gene: petF / Production host: Escherichia coli (E. coli) / References: UniProt: Q85FT5
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.5M ammonium sulfate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF
RadiationMonochromator: Confocal mirror / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 0.97→50 Å / Num. all: 57345 / Num. obs: 57345 / % possible obs: 96.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.53 % / Rmerge(I) obs: 0.604 / Rsym value: 0.066

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CRANKphasing
REFMAC5.7.0032refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: SAD / Resolution: 0.97→26.97 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.573 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17003 3081 5.1 %RANDOM
Rwork0.15073 ---
all0.1517 57345 --
obs0.1517 57345 96.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.618 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0 Å2
2--0.1 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 0.97→26.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms736 0 4 88 828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.02749
X-RAY DIFFRACTIONr_bond_other_d0.0030.02472
X-RAY DIFFRACTIONr_angle_refined_deg2.4451.9661012
X-RAY DIFFRACTIONr_angle_other_deg1.23431170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.943596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04527.14335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.01515129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3151
X-RAY DIFFRACTIONr_chiral_restr0.1620.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02843
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02130
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr7.87531221
X-RAY DIFFRACTIONr_sphericity_free32.538526
X-RAY DIFFRACTIONr_sphericity_bonded11.82751274
LS refinement shellResolution: 0.97→0.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 229 -
Rwork0.305 4096 -
obs--94.39 %

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