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- PDB-1j75: Crystal Structure of the DNA-Binding Domain Zalpha of DLM-1 Bound... -

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Basic information

Entry
Database: PDB / ID: 1j75
TitleCrystal Structure of the DNA-Binding Domain Zalpha of DLM-1 Bound to Z-DNA
Components
  • 5'-D(*TP*CP*GP*CP*GP*CP*G)-3'
  • Tumor Stroma and Activated Macrophage Protein DLM-1
KeywordsIMMUNE SYSTEM/DNA / PROTEIN-Z-DNA COMPLEX / IMMUNE SYSTEM-DNA COMPLEX
Function / homology
Function and homology information


left-handed Z-DNA binding / regulation of interleukin-1-mediated signaling pathway / double-stranded RNA adenosine deaminase activity / positive regulation of necroptotic process / positive regulation of type I interferon-mediated signaling pathway / pyroptotic inflammatory response / defense response to fungus / activation of innate immune response / positive regulation of inflammatory response / double-stranded RNA binding ...left-handed Z-DNA binding / regulation of interleukin-1-mediated signaling pathway / double-stranded RNA adenosine deaminase activity / positive regulation of necroptotic process / positive regulation of type I interferon-mediated signaling pathway / pyroptotic inflammatory response / defense response to fungus / activation of innate immune response / positive regulation of inflammatory response / double-stranded RNA binding / regulation of inflammatory response / defense response to virus / positive regulation of apoptotic process / innate immune response / apoptotic process / DNA binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Z-DNA-binding protein 1 / RHIM domain / RIP homotypic interaction motif / Z-DNA-binding domain in adenosine deaminases. / Z-binding domain profile. / Z-binding domain / Adenosine deaminase z-alpha domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Z-DNA-binding protein 1 / RHIM domain / RIP homotypic interaction motif / Z-DNA-binding domain in adenosine deaminases. / Z-binding domain profile. / Z-binding domain / Adenosine deaminase z-alpha domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / Z-DNA-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSchwartz, T. / Behlke, J. / Lowenhaupt, K. / Heinemann, U. / Rich, A.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structure of the DLM-1-Z-DNA complex reveals a conserved family of Z-DNA-binding proteins.
Authors: Schwartz, T. / Behlke, J. / Lowenhaupt, K. / Heinemann, U. / Rich, A.
History
DepositionMay 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_validate_close_contact / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*TP*CP*GP*CP*GP*CP*G)-3'
A: Tumor Stroma and Activated Macrophage Protein DLM-1


Theoretical massNumber of molelcules
Total (without water)9,4432
Polymers9,4432
Non-polymers00
Water1,838102
1
B: 5'-D(*TP*CP*GP*CP*GP*CP*G)-3'
A: Tumor Stroma and Activated Macrophage Protein DLM-1

B: 5'-D(*TP*CP*GP*CP*GP*CP*G)-3'
A: Tumor Stroma and Activated Macrophage Protein DLM-1


Theoretical massNumber of molelcules
Total (without water)18,8864
Polymers18,8864
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z+1/21
Unit cell
Length a, b, c (Å)63.611, 63.611, 72.238
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-391-

HOH

21A-335-

HOH

31A-338-

HOH

41A-339-

HOH

51A-399-

HOH

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Components

#1: DNA chain 5'-D(*TP*CP*GP*CP*GP*CP*G)-3'


Mass: 2114.398 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Tumor Stroma and Activated Macrophage Protein DLM-1


Mass: 7328.450 Da / Num. of mol.: 1 / Fragment: N-TERMINAL WINGED-HELIX DOMAIN ZALPHA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Novablue (DE3) / References: UniProt: Q9QY24
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15% PEG 4000, 0.1M ammonium hydrogen phosphate, 15% ethylene glycol, 0.1M MES pH 6.0, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2ammonium hydrogen phosphate11
3ethylene glycol11
4MES11
Crystal grow
*PLUS
Temperature: 24 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mMHEPES1drop
220 mM1dropNaCl
32 mMprotein1drop
415 %(w/v)PEG40001reservoir
5100 mMMES1reservoir
6100 mMammonium phosphate1reservoir
715 %(v/v)ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9102 / Wavelength: 0.9102 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 16, 2000
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9102 Å / Relative weight: 1
ReflectionResolution: 1.85→32 Å / Num. all: 7802 / Num. obs: 7802 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 23.4 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 6.7
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 2.9 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 182894
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameVersionClassification
EPMRphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QBJ

1qbj


Resolution: 1.85→32 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: CNS 1.0 and REFMAC5 used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.24 826 10.6 %RANDOM R VALUE (WORKING + TEST SET) : 0.22152
Rwork0.218 ---
all0.225 7778 --
obs0.225 7778 99.53 %-
Solvent computationSolvent model: BABINET MODEL WITH MASK PARAMETERS FOR MASK CALCULATION VDW PROBE RADIUS : 1.40 ION PROBE RADIUS : 0.80 SHRINKAGE RADIUS : 0.80
Displacement parametersBiso mean: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.85→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms444 140 0 102 686
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_bond_d_na0.0171.614
X-RAY DIFFRACTIONc_angle_deg1.592.603
X-RAY DIFFRACTIONc_angle_deg_na1.83.444
X-RAY DIFFRACTIONc_mcangle_it2.65.549
X-RAY DIFFRACTIONc_mcbond_it1.61
LS refinement shellResolution: 1.85→1.88 Å
RfactorNum. reflection% reflection
Rfree0.313 53 -
Rwork0.279 --
obs--99.5 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.6 % / Rfactor obs: 0.22152 / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.3 Å2
LS refinement shell
*PLUS
Rfactor Rfree: 0.313 / Rfactor Rwork: 0.279

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