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- PDB-3vk0: Crystal Structure of hypothetical transcription factor NHTF from ... -

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Basic information

Entry
Database: PDB / ID: 3vk0
TitleCrystal Structure of hypothetical transcription factor NHTF from Neisseria
ComponentsTranscriptional regulator
KeywordsDNA BINDING PROTEIN / HTH motif / XRE transcription factor
Function / homology
Function and homology information


DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
: / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsWang, H.-C. / Ko, T.-P. / Wu, M.-L. / Wu, H.-J. / Ku, S.-C. / 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 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Transcriptional regulator
B: Transcriptional regulator
C: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)39,2373
Polymers39,2373
Non-polymers00
Water4,306239
1
A: Transcriptional regulator

A: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)26,1582
Polymers26,1582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area1460 Å2
ΔGint-13 kcal/mol
Surface area9830 Å2
MethodPISA
2
B: Transcriptional regulator
C: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)26,1582
Polymers26,1582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-16 kcal/mol
Surface area9170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.013, 108.899, 44.083
Angle α, β, γ (deg.)90.00, 115.61, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-231-

HOH

21C-205-

HOH

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Components

#1: Protein Transcriptional regulator / NHTF


Mass: 13079.033 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: NMB1204 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7DDD9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.07 Å3/Da / Density % sol: 40.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.72M Sodium formate, 9% PEG8000, 9% PEG1000, 100mM Sodium acetate, pH 5.5, 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: Jul 23, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. all: 25961 / Num. obs: 25883 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 39.8
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B5A

2b5a


Resolution: 1.88→27.86 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.469 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22991 1314 5.1 %RANDOM
Rwork0.18194 ---
obs0.1844 24546 99.53 %-
all-24662 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.136 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20 Å2-0.44 Å2
2---1.51 Å20 Å2
3---2.52 Å2
Refinement stepCycle: LAST / Resolution: 1.88→27.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 0 239 2361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222150
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.992904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3285261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.623.33399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26415406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0911524
X-RAY DIFFRACTIONr_chiral_restr0.1130.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211593
X-RAY DIFFRACTIONr_mcbond_it1.1471.51319
X-RAY DIFFRACTIONr_mcangle_it1.98422105
X-RAY DIFFRACTIONr_scbond_it3.2123831
X-RAY DIFFRACTIONr_scangle_it5.1254.5799
LS refinement shellResolution: 1.879→1.928 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 85 -
Rwork0.276 1826 -
obs--98.96 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
1-8.598151.970635.9403
24.668732.093639.5107
32.240717.248823.4208
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 93
2X-RAY DIFFRACTION2B5 - 90
3X-RAY DIFFRACTION3C5 - 91

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