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- PDB-1dm9: HEAT SHOCK PROTEIN 15 KD -

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Basic information

Entry
Database: PDB / ID: 1dm9
TitleHEAT SHOCK PROTEIN 15 KD
ComponentsHYPOTHETICAL 15.5 KD PROTEIN IN MRCA-PCKA INTERGENIC REGION
KeywordsSTRUCTURAL GENOMICS / HEAT SHOCK PROTEINS / PROTEIN-RNA INTERACTIONS / RIBOSOME
Function / homology
Function and homology information


ribosomal large subunit binding / cellular response to heat / response to heat / single-stranded RNA binding / DNA binding / cytosol
Similarity search - Function
Heat shock protein 15 / RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S4 RNA-binding domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / S4 domain / S4 RNA-binding domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Heat shock protein 15
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsStaker, B.L. / Korber, P. / Bardwell, J.C.A. / Saper, M.A.
CitationJournal: EMBO J. / Year: 2000
Title: Structure of Hsp15 reveals a novel RNA-binding motif.
Authors: Staker, B.L. / Korber, P. / Bardwell, J.C. / Saper, M.A.
History
DepositionDec 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: HYPOTHETICAL 15.5 KD PROTEIN IN MRCA-PCKA INTERGENIC REGION
B: HYPOTHETICAL 15.5 KD PROTEIN IN MRCA-PCKA INTERGENIC REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6348
Polymers31,0582
Non-polymers5766
Water2,540141
1
A: HYPOTHETICAL 15.5 KD PROTEIN IN MRCA-PCKA INTERGENIC REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6252
Polymers15,5291
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HYPOTHETICAL 15.5 KD PROTEIN IN MRCA-PCKA INTERGENIC REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0096
Polymers15,5291
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.070, 67.930, 41.010
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 HYPOTHETICAL 15.5 KD PROTEIN IN MRCA-PCKA INTERGENIC REGION


Mass: 15528.927 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ACG8
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: AMMONIUM SULFATE, AMMONIUM ACETATE, GLYCEROL, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7
Details: drop consists of equal volume of protein and precipitant solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
111 mg/mlprotein1drop
220 mM1dropNaCl
31 mMEDTA1drop
450 mMHEPES1drop
52.0 Mammonium sulfate1reservoirprecipitant
60.1 Msodium acetate1reservoirprecipitant
710 %glycerol1reservoirprecipitant

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 22026 / Num. obs: 21673 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 30.677 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 7.23
Reflection shellResolution: 2→2.07 Å / Redundancy: 5 % / Rmerge(I) obs: 0.353 / % possible all: 88.9
Reflection shell
*PLUS
% possible obs: 88.9 % / Num. unique obs: 1911

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
bioteXdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2856 2062 -RANDOM
Rwork0.226 ---
obs0.226 20776 94.2 %-
all-22061 --
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1637 0 30 141 1808
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015829
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.60776
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg23.98432
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_d1.608
X-RAY DIFFRACTIONc_dihedral_angle_deg23.98
X-RAY DIFFRACTIONc_improper_angle_deg1.025
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.07 Å / Rfactor Rfree: 0.319 / Num. reflection Rfree: 178 / Rfactor Rwork: 0.294 / Num. reflection Rwork: 1729

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