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- PDB-1u00: HscA substrate binding domain complexed with the IscU recognition... -

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Basic information

Entry
Database: PDB / ID: 1u00
TitleHscA substrate binding domain complexed with the IscU recognition peptide ELPPVKIHC
Components
  • Chaperone protein hscA
  • IscU recognition peptide
KeywordsCHAPERONE / HscA / Hsc66 / DnaK / Hsp70 / IscU
Function / homology
Function and homology information


iron-sulfur cluster transfer complex / protein maturation by iron-sulfur cluster transfer / cellular response to cold / iron-sulfur cluster assembly / ADP binding / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
ISC system FeS cluster assembly, HscA chaperone / HscA chaperone, nucleotide-binding domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily ...ISC system FeS cluster assembly, HscA chaperone / HscA chaperone, nucleotide-binding domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / ATPase, nucleotide binding domain / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chaperone protein HscA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsCupp-Vickery, J.R. / Peterson, J.C. / Ta, D.T. / Vickery, L.E.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of the Molecular Chaperone HscA Substrate Binding Domain Complexed with the IscU Recognition Peptide ELPPVKIHC.
Authors: Cupp-Vickery, J.R. / Peterson, J.C. / Ta, D.T. / Vickery, L.E.
History
DepositionJul 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperone protein hscA
P: IscU recognition peptide


Theoretical massNumber of molelcules
Total (without water)25,4532
Polymers25,4532
Non-polymers00
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-10 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.761, 83.340, 128.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Chaperone protein hscA / / Hsc66


Mass: 24415.682 Da / Num. of mol.: 1 / Fragment: HscA substrate binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hscA / Plasmid: pTrc / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6Z1
#2: Protein/peptide IscU recognition peptide


Mass: 1037.274 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.8 Å3/Da / Density % sol: 55 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: potassium sodium tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→70 Å / Num. obs: 24950 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 9.4
Reflection shellHighest resolution: 1.95 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1609 / Rsym value: 0.358 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DnaK beta subdomain

Resolution: 1.95→70.71 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.65 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.131 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21038 2524 10.1 %RANDOM
Rwork0.17436 ---
all0.1779 ---
obs0.1779 22426 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.982 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å20 Å20 Å2
2--0.42 Å20 Å2
3---1.34 Å2
Refinement stepCycle: LAST / Resolution: 1.95→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1738 0 0 259 1997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0211757
X-RAY DIFFRACTIONr_bond_other_d0.0050.021658
X-RAY DIFFRACTIONr_angle_refined_deg2.1081.9592379
X-RAY DIFFRACTIONr_angle_other_deg1.02533836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9615234
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_restr0.1380.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021987
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02327
X-RAY DIFFRACTIONr_nbd_refined0.2580.2367
X-RAY DIFFRACTIONr_nbd_other0.2910.21810
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0960.2956
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2142
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0980.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3490.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2710.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.4511.51172
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.54921865
X-RAY DIFFRACTIONr_scbond_it4.3133585
X-RAY DIFFRACTIONr_scangle_it7.2124.5514
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.247 196
Rwork0.204 1609

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