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- PDB-1f30: THE STRUCTURAL BASIS FOR DNA PROTECTION BY E. COLI DPS PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1f30
TitleTHE STRUCTURAL BASIS FOR DNA PROTECTION BY E. COLI DPS PROTEIN
ComponentsDNA PROTECTION DURING STARVATION PROTEIN
KeywordsDNA BINDING PROTEIN / Dodecamer
Function / homology
Function and homology information


DnaA-Dps complex / Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / chromosome condensation / response to stress / response to starvation / negative regulation of DNA-templated DNA replication initiation / ferric iron binding / intracellular iron ion homeostasis ...DnaA-Dps complex / Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / chromosome condensation / response to stress / response to starvation / negative regulation of DNA-templated DNA replication initiation / ferric iron binding / intracellular iron ion homeostasis / DNA binding / identical protein binding / membrane / 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: 2.85 Å
AuthorsLuo, J. / Liu, D. / White, M.A. / Fox, R.O.
CitationJournal: To be Published
Title: The Structural Basis for DNA Protection by E. coli Dps Protein
Authors: Luo, J. / Liu, D. / White, M.A. / Fox, R.O.
History
DepositionMay 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: 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)226,89436
Polymers224,64412
Non-polymers2,25124
Water9,710539
1
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
hetero molecules

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,89436
Polymers224,64412
Non-polymers2,25124
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area50430 Å2
ΔGint-558 kcal/mol
Surface area53200 Å2
MethodPISA
2
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

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)226,89436
Polymers224,64412
Non-polymers2,25124
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area50630 Å2
ΔGint-555 kcal/mol
Surface area52710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.773, 140.780, 268.419
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein
DNA PROTECTION DURING STARVATION PROTEIN / DPS


Mass: 18720.295 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DPS / Plasmid: PET32A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P0ABT2
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


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


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.5 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 10mM MOPS, 100mM KCl, 10% glycerol + 100mM TrisHCL, 100mM KCl, 10% glycerol, 11% PEG 8000, and 5mM DTT, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.1
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Jun 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→90 Å / Num. all: 204562 / Num. obs: 51548 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.97 % / Biso Wilson estimate: 60 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.3
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.235 / Num. unique all: 2581 / % possible all: 99.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS0.3refinement
CNS0.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DPS D75C,D78A UNPUBLISHED STRUCTURE

Resolution: 2.85→29.47 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 7458639.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 5070 10.1 %THIN SHELLS
Rwork0.232 ---
obs0.232 50349 96.1 %-
all-50349 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.73 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso mean: 63.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.57 Å20 Å2
3----0.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.85→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14832 0 108 539 15479
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_d17.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.942
X-RAY DIFFRACTIONc_scbond_it1.522
X-RAY DIFFRACTIONc_scangle_it2.462.5
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDRms dev position (Å)Weight Biso
11X-RAY DIFFRACTION15012
22X-RAY DIFFRACTION12
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.387 771 10.2 %
Rwork0.332 6815 -
obs--87.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3TRS.PARAMTRS.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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