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- PDB-1dps: THE CRYSTAL STRUCTURE OF DPS, A FERRITIN HOMOLOG THAT BINDS AND P... -

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Basic information

Entry
Database: PDB / ID: 1dps
TitleTHE CRYSTAL STRUCTURE OF DPS, A FERRITIN HOMOLOG THAT BINDS AND PROTECTS DNA
ComponentsDPS
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / FERRITIN / IRON SEQUESTRATION / STATIONARY PHASE / OXIDATIVE DAMAGE
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 / MIR, NCS / Resolution: 1.6 Å
AuthorsGrant, R.A. / Filman, D.J. / Finkel, S.E. / Kolter, R. / Hogle, J.M.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: The crystal structure of Dps, a ferritin homolog that binds and protects DNA.
Authors: Grant, R.A. / Filman, D.J. / Finkel, S.E. / Kolter, R. / Hogle, J.M.
History
DepositionFeb 23, 1998Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_keywords / 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 / _pdbx_database_status.process_site / _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.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.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.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_keywords.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DPS
B: DPS
C: DPS
D: DPS
E: DPS
F: DPS
G: DPS
H: DPS
I: DPS
J: DPS
K: DPS
L: DPS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,11224
Polymers224,83612
Non-polymers27612
Water25,1671397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45690 Å2
ΔGint-234 kcal/mol
Surface area56700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.410, 139.650, 118.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999989, 0.000512, -0.004563), (-0.000489, -0.999987, -0.005008), (-0.004566, -0.005006, 0.999977)56.4519, 70.0592, 0.3344
2given(-0.997483, 0.070904, -0.000243), (0.070904, 0.997482, 0.001743), (0.000366, 0.001721, -0.999998)53.6743, -1.8928, 59.1023
3given(0.997699, -0.067669, 0.004198), (-0.067658, -0.997705, -0.002665), (0.004368, 0.002374, -0.999988)2.287, 71.7675, 58.9011
4given(0.032708, 0.998898, 0.033657), (-0.003638, -0.033556, 0.99943), (0.999458, -0.032812, 0.002536)-8.5598, 6.6729, 2.6547
5given(-0.036746, -0.998857, -0.030584), (0.00197, 0.030532, -0.999532), (0.999323, -0.036789, 0.000845)65.1769, 63.2303, 2.7164
6given(-0.032294, -0.999068, 0.028622), (0.001782, 0.02858, 0.99959), (-0.999477, 0.032332, 0.000858)63.227, 4.3372, 56.5471
7given(0.036552, 0.998973, -0.026766), (0.003199, -0.026901, -0.999633), (-0.999327, 0.036453, -0.004179)-6.8117, 65.1924, 56.4655
8given(0.023099, -0.0046, 0.999723), (0.999095, -0.035611, -0.023248), (0.035708, 0.999355, 0.003773)-1.5746, 8.6354, -6.4992
9given(-0.033176, -0.000273, -0.999449), (-0.998911, 0.032829, 0.033149), (0.032802, 0.999461, -0.001362)58.5808, 60.8805, -6.2608
10given(0.034648, 0.003681, -0.999393), (0.998929, -0.030795, 0.034518), (-0.03065, -0.999519, -0.004744)56.601, 6.7833, 65.3942
11given(-0.030572, 0.000474, 0.999532), (-0.99893, 0.034718, -0.03057), (-0.034716, -0.999397, -0.000588)-0.3539, 62.6733, 65.5028

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Components

#1: Protein
DPS / PEXB


Mass: 18736.359 Da / Num. of mol.: 12 / Mutation: S164C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ZK126 DPS\:\:KAN / Gene: DPS / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABT2
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1397 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 53 % / Description: FUJI IMAGE PLATES FOR CHESS DATA
Crystal growpH: 8
Details: 1.55-1.7 M SODIUM FORMATE 13-16% PEG 8000 100 MM NACL 50 MM TRIS PH 8, pH 8.0

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 1792266 / % possible obs: 92 % / Biso Wilson estimate: 20.2 Å2 / Rsym value: 0.046 / Net I/σ(I): 14.2
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.052 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.052 / % possible all: 80.1

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR, NCS / Resolution: 1.6→20 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.22 22050 9.9 %RANDOM
Rwork0.188 ---
obs0.188 221900 76.3 %-
Displacement parametersBiso mean: 18.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14698 0 12 1397 16107
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.55
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.238 2817 10.1 %
Rwork0.232 25150 -
obs--58.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLWAT_4PDB.TOPOLOGY
X-RAY DIFFRACTION3NAI.PAR

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