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- PDB-3b2g: Leptolyngbya boryana Ferredoxin -

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Basic information

Entry
Database: PDB / ID: 3b2g
TitleLeptolyngbya boryana Ferredoxin
ComponentsFerredoxin-1
KeywordsELECTRON TRANSPORT / electron transfer / FNR / NiR / SiR / Fd-GOGAT
Function / homology
Function and homology information


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-1
Similarity search - Component
Biological speciesLeptolyngbya boryana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsKurisu, G. / Hase, T.
CitationJournal: J.Biochem. / Year: 2012
Title: A new structural insight into differential interaction of cyanobacterial and plant ferredoxins with nitrite reductase as revealed by NMR and X-ray crystallographic studies
Authors: Sakakibara, Y. / Kimura, H. / Iwamura, A. / Saitoh, T. / Ikegami, T. / Kurisu, G. / Hase, T.
History
DepositionAug 1, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_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

Downloads & links

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Assembly

Deposited unit
A: Ferredoxin-1
B: Ferredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5934
Polymers21,2412
Non-polymers3522
Water4,017223
1
A: Ferredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7962
Polymers10,6211
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ferredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7962
Polymers10,6211
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.141, 34.158, 48.604
Angle α, β, γ (deg.)90.00, 107.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-124-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: FES / End label comp-ID: FES / Refine code: 5 / Auth seq-ID: 1 - 99 / Label seq-ID: 1

Dom-IDAuth asym-IDLabel asym-ID
1AA - C
2BB - D

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Components

#1: Protein Ferredoxin-1 / / Ferredoxin I / FdI


Mass: 10620.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptolyngbya boryana (bacteria) / Gene: petF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q51577
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.02 Å3/Da / Density % sol: 39.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 2.2M Ammonium Sulfate, 0.1M sodium citrate, , pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 17174 / Num. obs: 16985 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→27.83 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.87 / SU B: 4.714 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24757 540 3.2 %RANDOM
Rwork0.18329 ---
all0.18515 16985 --
obs0.18515 16442 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.651 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--0.06 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.76→27.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1484 0 8 223 1715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221514
X-RAY DIFFRACTIONr_angle_refined_deg1.581.9742066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5095194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80327.22272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83415234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.208152
X-RAY DIFFRACTIONr_chiral_restr0.0980.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021154
X-RAY DIFFRACTIONr_nbd_refined0.2210.2748
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21059
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2520.2170
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4640.256
X-RAY DIFFRACTIONr_mcbond_it0.5661.5999
X-RAY DIFFRACTIONr_mcangle_it0.98521582
X-RAY DIFFRACTIONr_scbond_it1.8443572
X-RAY DIFFRACTIONr_scangle_it3.0154.5480
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
392medium positional0.230.5
354loose positional0.955
392medium thermal0.712
354loose thermal1.4510
LS refinement shellResolution: 1.757→1.802 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 47 -
Rwork0.175 1153 -
obs--93.1 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7260.0020.0950.68810.25660.91660.0120.0246-0.01810.01520.0237-0.04160.00470.0753-0.0357-0.01870.00470.0016-0.02310.0016-0.018433.612-0.06818.568
20.84530.00710.13570.69140.23331.1497-0.03110.03890.03570.00630.02470.0154-0.0426-0.01310.0064-0.013-0.00350.0018-0.03180.0046-0.029312.9222.4855.256
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 98
2X-RAY DIFFRACTION2B1 - 98

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