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- PDB-3w1o: Neisseria DNA mimic protein DMP12 -

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Basic information

Entry
Database: PDB / ID: 3w1o
TitleNeisseria DNA mimic protein DMP12
ComponentsDNA mimic protein DMP12
KeywordsPROTEIN BINDING / DNA mimic / Hu protein
Function / homologyHypothetical protein yfbM fold - #20 / DNA-mimic protein DMP12 / DNA-mimic protein DMP12 superfamily / DNA-mimic protein / Hypothetical protein yfbM fold / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / MafB alternative c terminus
Function and homology information
Biological speciesNeisseria meningitidis MC58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsWang, H.C. / Ko, T.P. / Wu, M.L. / Wang, A.H.J.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Neisseria conserved hypothetical protein DMP12 is a DNA mimic that binds to histone-like HU protein
Authors: Wang, H.C. / Wu, M.L. / Ko, T.P. / Wang, A.H.
History
DepositionNov 19, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Structure summary / Category: entity / software / struct
Item: _entity.pdbx_description / _software.classification ..._entity.pdbx_description / _software.classification / _software.name / _software.version / _struct.pdbx_descriptor
Revision 1.3Mar 20, 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_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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA mimic protein DMP12
B: DNA mimic protein DMP12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1944
Polymers28,1462
Non-polymers492
Water5,639313
1
A: DNA mimic protein DMP12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0972
Polymers14,0731
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA mimic protein DMP12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0972
Polymers14,0731
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-16 kcal/mol
Surface area10920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.519, 112.519, 57.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein DNA mimic protein DMP12


Mass: 14072.884 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Strain: MC58 / Gene: NMB2123 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9JXC6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 3.21 Å3/Da / Density % sol: 61.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Magnesium acetate 0.1M Sodium cacodylate 20% PEG8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2011
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 31241 / Num. obs: 30304 / % possible obs: 97 % / Observed criterion σ(F): 0.3 / Observed criterion σ(I): 3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 32.7
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.7 / % possible all: 97.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHELXCDphasing
SHELXEmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.398 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21825 1540 5.1 %RANDOM
Rwork0.18564 ---
all0.18734 29907 --
obs0.18734 28738 96.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.062 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1916 0 2 313 2231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221958
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9362660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7215228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.17826100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00315358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.616154
X-RAY DIFFRACTIONr_chiral_restr0.1220.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021462
X-RAY DIFFRACTIONr_mcbond_it1.2161.51148
X-RAY DIFFRACTIONr_mcangle_it2.21221882
X-RAY DIFFRACTIONr_scbond_it3.2723810
X-RAY DIFFRACTIONr_scangle_it5.394.5778
LS refinement shellResolution: 1.85→1.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 111 -
Rwork0.243 1893 -
all-2004 -
obs--86.23 %

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