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- PDB-5ffi: [2Fe:2S] ferredoxin FeSII from Azotobacter vinelandii -

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Basic information

Entry
Database: PDB / ID: 5ffi
Title[2Fe:2S] ferredoxin FeSII from Azotobacter vinelandii
ComponentsDimeric (2Fe-2S) protein
KeywordsMETAL BINDING PROTEIN / ferredoxin / nitrogen fixation / Shethna protein II / FeSII / nitrogenase
Function / homology
Function and homology information


nitrogen fixation / 2 iron, 2 sulfur cluster binding / metal ion binding / cytoplasm
Similarity search - Function
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 / Protein FeSII
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.17 Å
AuthorsSchlesier, J. / Rohde, M. / Gerhardt, S. / Einsle, O.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationRTG 1976 Germany
European Research Council310656 Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: A Conformational Switch Triggers Nitrogenase Protection from Oxygen Damage by Shethna Protein II (FeSII).
Authors: Schlesier, J. / Rohde, M. / Gerhardt, S. / Einsle, O.
History
DepositionDec 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Mar 29, 2017Group: Other
Revision 1.3May 10, 2017Group: Data collection
Revision 1.4Jun 7, 2017Group: Data collection
Revision 1.5May 8, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dimeric (2Fe-2S) protein
B: Dimeric (2Fe-2S) protein
C: Dimeric (2Fe-2S) protein
D: Dimeric (2Fe-2S) protein
E: Dimeric (2Fe-2S) protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,32610
Polymers66,4475
Non-polymers8795
Water2,738152
1
B: Dimeric (2Fe-2S) protein
hetero molecules

A: Dimeric (2Fe-2S) protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9304
Polymers26,5792
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
MethodPISA
2
A: Dimeric (2Fe-2S) protein
hetero molecules

B: Dimeric (2Fe-2S) protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9304
Polymers26,5792
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area2530 Å2
ΔGint-44 kcal/mol
Surface area13490 Å2
MethodPISA
3
D: Dimeric (2Fe-2S) protein
hetero molecules

C: Dimeric (2Fe-2S) protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9304
Polymers26,5792
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
MethodPISA
4
C: Dimeric (2Fe-2S) protein
hetero molecules

D: Dimeric (2Fe-2S) protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9304
Polymers26,5792
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area2570 Å2
ΔGint-43 kcal/mol
Surface area13680 Å2
MethodPISA
5
E: Dimeric (2Fe-2S) protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4652
Polymers13,2891
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.271, 134.480, 36.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Dimeric (2Fe-2S) protein / Ferredoxin FeSII


Mass: 13289.330 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q44501
#2: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1 M of tri-sodium citrate 0.01 M sodium tetraborate (Na2B4O7)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0003 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 2, 2015
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0003 Å / Relative weight: 1
ReflectionResolution: 2.169→94.66 Å / Num. obs: 36128 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 42.92 Å2 / Rmerge(I) obs: 0.149 / Rsym value: 0.149 / Net I/σ(I): 13.2
Reflection shellResolution: 2.169→2.177 Å / Redundancy: 12.5 % / Rmerge(I) obs: 1.38 / Mean I/σ(I) obs: 2.2 / Rsym value: 1.38 / % possible all: 100

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Processing

Software
NameVersionClassification
autoPROCdata reduction
XDS(VERSION March 1)data reduction
Aimless(version 0.5.12)data scaling
autoSHARPphasing
BUSTER2.10.2refinement
CCP46.5data scaling
RefinementResolution: 2.17→94.66 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.9257 / SU R Cruickshank DPI: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.218 / SU Rfree Blow DPI: 0.176 / SU Rfree Cruickshank DPI: 0.175
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 1687 4.68 %RANDOM
Rwork0.1952 ---
obs0.1967 36023 99.99 %-
Displacement parametersBiso mean: 59.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.7006 Å20 Å20 Å2
2--3.7469 Å20 Å2
3----3.0462 Å2
Refine analyzeLuzzati coordinate error obs: 0.298 Å
Refinement stepCycle: LAST / Resolution: 2.17→94.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4357 0 20 152 4529
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094435HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.125975HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1589SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes115HARMONIC2
X-RAY DIFFRACTIONt_gen_planes621HARMONIC5
X-RAY DIFFRACTIONt_it4435HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.19
X-RAY DIFFRACTIONt_other_torsion18.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion590SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4767SEMIHARMONIC4
LS refinement shellResolution: 2.17→2.23 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2046 151 5.29 %
Rwork0.2087 2702 -
all0.2085 2853 -
obs--99.93 %
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)
11.5269-1.24680.10162.2410.52630.94660.01020.06170.0126-0.02850.1750.26390.14660.0318-0.1852-0.02260.0329-0.1089-0.14830.037-0.0415-27.190545.6631-8.133
21.0546-1.8857-0.20583.62790.43140.73830.1594-0.102-0.2124-0.3382-0.04270.1925-0.03720.0687-0.1168-0.02710.0155-0.0133-0.13620.0663-0.045-20.45336.81997.4317
31.7619-1.0658-0.26953.4693-1.33244.39580.06330.00150.4983-0.04070.1065-0.0626-0.6109-1.0186-0.1697-0.24960.1624-0.0075-0.0852-0.103-0.0435-50.542620.5945-0.281
46.504-2.0102-0.75511.28630.46433.04120.30850.40190.4556-0.1769-0.0722-0.1397-0.3311-0.3652-0.2363-0.16360.05040.0217-0.18320.0186-0.101-40.864715.0282-16.0244
57.72251.51091.97612.3023-0.20351.3308-0.31670.14460.4582-0.23080.24510.33080.02770.07870.0716-0.14720.0276-0.0485-0.09210.0327-0.0383-12.69823.40658.9114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }

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