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- PDB-1r95: Crystal Structure of IscA (native) -

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Basic information

Entry
Database: PDB / ID: 1r95
TitleCrystal Structure of IscA (native)
ComponentsProtein yfhF
KeywordsMETAL TRANSPORT / TETRAMERIC / BETA BARREL / IRON-SULFUR CLUSTER PROTEIN / PSEUDO-ASYMMETRIC MOTIFS
Function / homology
Function and homology information


iron-sulfur cluster transfer complex / iron chaperone activity / iron-sulfur cluster assembly / ferrous iron binding / 2 iron, 2 sulfur cluster binding / cytosol / cytoplasm
Similarity search - Function
Iron-binding protein IscA, proteobacteria / : / FeS cluster insertion, C-terminal, conserved site / Hypothetical hesB/yadR/yfhF family signature. / FeS cluster insertion protein / Hypothetical Protein Aq_1857; Chain: A; / HesB-like domain / FeS cluster biogenesis / HesB-like domain superfamily / Iron-sulphur cluster biosynthesis ...Iron-binding protein IscA, proteobacteria / : / FeS cluster insertion, C-terminal, conserved site / Hypothetical hesB/yadR/yfhF family signature. / FeS cluster insertion protein / Hypothetical Protein Aq_1857; Chain: A; / HesB-like domain / FeS cluster biogenesis / HesB-like domain superfamily / Iron-sulphur cluster biosynthesis / Sandwich / Mainly Beta
Similarity search - Domain/homology
Iron-binding protein IscA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SIR / Resolution: 2.65 Å
AuthorsBilder, P.W. / Ding, H. / Newcomer, M.E.
CitationJournal: Biochemistry / Year: 2004
Title: Crystal structure of the ancient, Fe-S scaffold IscA reveals a novel protein fold.
Authors: Bilder, P.W. / Ding, H. / Newcomer, M.E.
History
DepositionOct 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein yfhF
B: Protein yfhF


Theoretical massNumber of molelcules
Total (without water)25,6872
Polymers25,6872
Non-polymers00
Water1,09961
1
A: Protein yfhF
B: Protein yfhF

A: Protein yfhF
B: Protein yfhF


Theoretical massNumber of molelcules
Total (without water)51,3744
Polymers51,3744
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_775-x+2,-y+2,z1
Unit cell
Length a, b, c (Å)55.527, 55.527, 159.037
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 1 / Auth seq-ID: 1 - 97 / Label seq-ID: 1 - 97

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological assembly comprises two possible tetramers (A,B). tetramer A is generated from either monomer in asymmetric unit using the following symmetry operators: -x,-y, z and -y,x-y,z+2/3 and y,-x+y,z+2/3. Tetramer B is generated from the dimer in the asymmetric unit and the symmetry operator -x,-y,z.

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Components

#1: Protein Protein yfhF


Mass: 12843.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YFHF, B2528, C3053, Z3795, ECS3394, SF2575, S2747 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AAC8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 298 K / pH: 8
Details: dibasic ammonium phosphate, imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.00
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
117 mg/mlprotein1drop
21.1 mMferrous ammonium sulfate1drop
32 mMdithiothreitol1drop
40.8-1.0 Mdibasic ammonium phosphate1reservoir
50.1 Mimidazole1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 31, 2003
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→500 Å / Num. obs: 8034 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 56.6 Å2 / Rsym value: 0.066 / Net I/σ(I): 58
Reflection shellResolution: 2.65→2.75 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.479 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.65 Å / Lowest resolution: 9999 Å / Num. measured all: 77724 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.479

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: SIR / Resolution: 2.65→27.32 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.894 / SU B: 7.844 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.703 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.256 378 4.9 %RANDOM
Rwork0.232 ---
obs0.234 7371 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.65→27.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1468 0 0 61 1529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221492
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.9692010
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4425192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021136
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.2641
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.271.5954
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.43721526
X-RAY DIFFRACTIONr_scbond_it2.7843538
X-RAY DIFFRACTIONr_scangle_it5.2334.5484
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Ens-ID: 1 / Number: 735 / Refine-ID: X-RAY DIFFRACTION

Dom-IDTypeRms dev position (Å)Weight position
1tight positional0.010.05
2tight thermal0.030.5
LS refinement shellResolution: 2.65→2.72 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.248 17
Rwork0.316 495
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 27 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.4

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