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- PDB-3vjz: Crystal structure of the DNA mimic protein DMP19 -

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Basic information

Entry
Database: PDB / ID: 3vjz
TitleCrystal structure of the DNA mimic protein DMP19
ComponentsPutative uncharacterized protein
KeywordsGENE REGULATION / helix bundle / DNA mimic
Function / homologyA middle domain of Talin 1 - #60 / Domain of unknown function DUF4375 / DMP19-like protein / A middle domain of Talin 1 / Up-down Bundle / Mainly Alpha / DNA mimic protein DMP19
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.8 Å
AuthorsWang, H.-C. / Ko, T.-P. / Wang, A.H.-J.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Neisseria conserved protein DMP19 is a DNA mimic protein that prevents DNA binding to a hypothetical nitrogen-response transcription factor
Authors: Wang, H.-C. / Ko, T.-P. / Wu, M.-L. / Ku, S.-C. / Wu, H.-J. / Wang, A.H.-J.
History
DepositionNov 1, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)37,3332
Polymers37,3332
Non-polymers00
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-37 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.878, 65.309, 59.094
Angle α, β, γ (deg.)90.00, 99.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative uncharacterized protein / DMP19


Mass: 18666.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: NMB0541 / Plasmid: pEt16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9K0P4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 2M Ammonium sulfate, 200mM Potassium sodium tartrate tetrahydrate, 100mM Sodium citrate tribasic dihydrate, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418, 1.0397, 1.0229, 1.0400
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 28, 2010 / Details: mirrors
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.03971
31.02291
41.041
ReflectionResolution: 1.8→30 Å / Num. all: 30584 / Num. obs: 30584 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 9.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 47.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.874 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3027 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2096 1457 RANDOM
Rwork0.1698 --
all0.1716 30569 -
obs0.1716 29620 -
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2596 0 0 387 2983
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.77456
X-RAY DIFFRACTIONc_bond_d0.018118
LS refinement shellResolution: 1.8→1.86 Å
RfactorNum. reflection% reflection
Rfree0.3399 133 -
Rwork0.2787 --
obs-2692 88.76 %

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