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- PDB-1l8h: DNA PROTECTION AND BINDING BY E. COLI DPS PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1l8h
TitleDNA PROTECTION AND BINDING BY E. COLI DPS PROTEIN
ComponentsDNA PROTECTION DURING STARVATION PROTEIN
KeywordsDNA BINDING PROTEIN / DODECAMER / METAL BOUND COMPLEX
Function / homology
Function and homology information


DnaA-Dps complex / Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / chromosome condensation / response to starvation / negative regulation of DNA-templated DNA replication initiation / ferric iron binding / intracellular iron ion homeostasis / DNA binding ...DnaA-Dps complex / Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / chromosome condensation / response to starvation / negative regulation of DNA-templated DNA replication initiation / ferric iron binding / intracellular iron ion homeostasis / DNA binding / membrane / identical protein binding / cytoplasm
Similarity search - Function
DNA protection during starvation protein, gammaproteobacteria / Dps protein family signature 2. / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like ...DNA protection during starvation protein, gammaproteobacteria / Dps protein family signature 2. / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA protection during starvation protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLuo, J. / Liu, D. / White, M.A. / Fox, R.O.
CitationJournal: To be Published
Title: DNA Protection and Binding by E. Coli Dps Protein
Authors: Luo, J. / Liu, D. / White, M.A. / Fox, R.O.
History
DepositionMar 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA PROTECTION DURING STARVATION PROTEIN
B: DNA PROTECTION DURING STARVATION PROTEIN
C: DNA PROTECTION DURING STARVATION PROTEIN
D: DNA PROTECTION DURING STARVATION PROTEIN
E: DNA PROTECTION DURING STARVATION PROTEIN
F: DNA PROTECTION DURING STARVATION PROTEIN
G: DNA PROTECTION DURING STARVATION PROTEIN
H: DNA PROTECTION DURING STARVATION PROTEIN
I: DNA PROTECTION DURING STARVATION PROTEIN
J: DNA PROTECTION DURING STARVATION PROTEIN
K: DNA PROTECTION DURING STARVATION PROTEIN
L: DNA PROTECTION DURING STARVATION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,90736
Polymers223,97212
Non-polymers1,93524
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49380 Å2
ΔGint-106 kcal/mol
Surface area53900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.265, 91.265, 239.714
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsThe dodecamer is the biological assembly

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Components

#1: Protein
DNA PROTECTION DURING STARVATION PROTEIN


Mass: 18664.340 Da / Num. of mol.: 12 / Mutation: D75C/D78A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABT2
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 10MM MOPS, 100MM KCL, 10%GLYCEROL + 100MM TRISHCL, 100MM KCL, 10% GLYCEROL, 11% PEG 8000, AND 5MM DTT, pH 8.10, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 4, 1998
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 37803 / Num. obs: 36212 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.074
Reflection shellResolution: 3.2→3.28 Å / Rmerge(I) obs: 0.35 / % possible all: 99.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1refinement
CNS1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F33

1f33


Resolution: 3.2→44.83 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3697305.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: eng and huber / Details: weighted R=18.5%
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1834 5.1 %SHELLS
Rwork0.21 ---
all0.21678 37792 --
obs0.21 35985 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.5207 Å2 / ksol: 0.345042 e/Å3
Displacement parametersBiso mean: 57.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å24.7 Å20 Å2
2---0.52 Å20 Å2
3---1.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.63 Å
Refinement stepCycle: LAST / Resolution: 3.2→44.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14727 0 108 114 14949
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it1.552
X-RAY DIFFRACTIONc_scangle_it2.622.5
LS refinement shellResolution: 3.2→3.26 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 99 5.7 %
Rwork0.342 1636 -
obs--91.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4LIGAND.PARAMLIGAND.TOP

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