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- PDB-1hlv: CRYSTAL STRUCTURE OF CENP-B(1-129) COMPLEXED WITH THE CENP-B BOX DNA -

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Basic information

Entry
Database: PDB / ID: 1hlv
TitleCRYSTAL STRUCTURE OF CENP-B(1-129) COMPLEXED WITH THE CENP-B BOX DNA
Components
  • (CENP-B BOX DNA) x 2
  • MAJOR CENTROMERE AUTOANTIGEN B
KeywordsDNA BINDING PROTEIN/DNA / HELIX-TURN-HELIX / PROTEIN-DNA COMPLEX / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


satellite DNA binding / centromeric DNA binding / condensed chromosome, centromeric region / chromosome, centromeric region / pericentric heterochromatin / chromosome / sequence-specific DNA binding / nuclear body / chromatin binding / DNA binding ...satellite DNA binding / centromeric DNA binding / condensed chromosome, centromeric region / chromosome, centromeric region / pericentric heterochromatin / chromosome / sequence-specific DNA binding / nuclear body / chromatin binding / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Centromere protein CENP-B, C-terminal domain / CENP-B, dimerisation domain superfamily / Centromere protein B dimerisation domain / CENP-B N-terminal DNA-binding domain / DNA binding HTH domain, Psq-type / Psq-type HTH domain profile. / DDE superfamily endonuclease domain / HTH CenpB-type DNA-binding domain / DDE superfamily endonuclease / Tc5 transposase DNA-binding domain ...Centromere protein CENP-B, C-terminal domain / CENP-B, dimerisation domain superfamily / Centromere protein B dimerisation domain / CENP-B N-terminal DNA-binding domain / DNA binding HTH domain, Psq-type / Psq-type HTH domain profile. / DDE superfamily endonuclease domain / HTH CenpB-type DNA-binding domain / DDE superfamily endonuclease / Tc5 transposase DNA-binding domain / CENPB-type HTH domain profile. / Putative DNA-binding domain in centromere protein B, mouse jerky and transposases. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Major centromere autoantigen B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsTanaka, Y. / Nureki, O. / Kurumizaka, H. / Fukai, S. / Kawaguchi, S. / Ikuta, M. / Iwahara, J. / Okazaki, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: EMBO J. / Year: 2001
Title: Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA.
Authors: Tanaka, Y. / Nureki, O. / Kurumizaka, H. / Fukai, S. / Kawaguchi, S. / Ikuta, M. / Iwahara, J. / Okazaki, T. / Yokoyama, S.
History
DepositionDec 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

Downloads & links

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Assembly

Deposited unit
B: CENP-B BOX DNA
C: CENP-B BOX DNA
A: MAJOR CENTROMERE AUTOANTIGEN B


Theoretical massNumber of molelcules
Total (without water)28,0563
Polymers28,0563
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.374, 83.374, 139.021
Angle α, β, γ (deg.)90, 90, 120
Int Tables number151
Space group name H-MP3112

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Components

#1: DNA chain CENP-B BOX DNA


Mass: 6494.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.
#2: DNA chain CENP-B BOX DNA


Mass: 6392.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.
#3: Protein MAJOR CENTROMERE AUTOANTIGEN B / CENP-B


Mass: 15169.706 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENP-B / Plasmid: PET15D / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P07199
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 4.88 Å3/Da / Density % sol: 74.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, potassium cacodylate, magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2potassium cacodylate11
3MgCl211
4MPD12
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13-6 mg/mlprotein1drop
2100 mMsodium acetate1reservoir
350 mMsodium cacodylate1reservoirpH6.5
415 %1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 10, 1999
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 19313 / Num. obs: 19313 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.9 % / Biso Wilson estimate: 58.195 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 13.9
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.216 / Rsym value: 0.216 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 19126 / % possible obs: 98.5 % / Num. measured all: 619774 / Rmerge(I) obs: 0.049

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.5→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2599 940 -RANDOM
Rwork0.2219 ---
all0.2219 19313 --
obs0.2219 19313 99.5 %-
Displacement parametersBiso mean: 45.8703 Å2
Baniso -1Baniso -2Baniso -3
1--5.82 Å2-4.385 Å20 Å2
2---5.82 Å20 Å2
3---11.639 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1066 855 0 98 2019
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.07324
X-RAY DIFFRACTIONc_bond_d0.005558
X-RAY DIFFRACTIONc_dihedral_angle_d18.42049
X-RAY DIFFRACTIONc_improper_angle_d1.27355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-ID% reflection obs (%)
2.5-2.590.3931870.3484X-RAY DIFFRACTION0.976
2.59-2.690.3441040.3204X-RAY DIFFRACTION0.998
2.69-2.820.3053860.2793X-RAY DIFFRACTION0.9953
2.82-2.960.3659970.3077X-RAY DIFFRACTION0.9985
2.96-3.150.3268850.2693X-RAY DIFFRACTION0.999
3.15-3.390.25681050.2201X-RAY DIFFRACTION0.9985
3.39-3.730.2872950.2454X-RAY DIFFRACTION1
3.73-4.270.2163970.2013X-RAY DIFFRACTION1
4.27-5.380.2383860.1788X-RAY DIFFRACTION0.9994
5.38-300.2027980.1723X-RAY DIFFRACTION0.9896
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.2253 / Rfactor Rfree: 0.2653
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.42049
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.27355
LS refinement shell
*PLUS
Highest resolution: 2.5 Å

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