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- PDB-1ufi: Crystal structure of the dimerization domain of human CENP-B -

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Basic information

Entry
Database: PDB / ID: 1ufi
TitleCrystal structure of the dimerization domain of human CENP-B
ComponentsMajor centromere autoantigen B
KeywordsDNA BINDING PROTEIN / dimerization domain / salt bridge / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
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
Dimerisation domain of CENP-B / 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 ...Dimerisation domain of CENP-B / 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. / Homeobox-like domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Major centromere autoantigen B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsTawaramoto, M.S. / Kurumizaka, H. / Tanaka, Y. / Park, S.-Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of the human centromere protein B (CENP-B) dimerization domain at 1.65-A resolution
Authors: Tawaramoto, M.S. / Park, S.-Y. / Tanaka, Y. / Nureki, O. / Kurumizaka, H. / Yokoyama, S.
History
DepositionMay 30, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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: Major centromere autoantigen B
B: Major centromere autoantigen B
C: Major centromere autoantigen B
D: Major centromere autoantigen B


Theoretical massNumber of molelcules
Total (without water)28,9974
Polymers28,9974
Non-polymers00
Water2,648147
1
A: Major centromere autoantigen B
B: Major centromere autoantigen B


Theoretical massNumber of molelcules
Total (without water)14,4992
Polymers14,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-28 kcal/mol
Surface area5620 Å2
MethodPISA
2
C: Major centromere autoantigen B
D: Major centromere autoantigen B


Theoretical massNumber of molelcules
Total (without water)14,4992
Polymers14,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-27 kcal/mol
Surface area6060 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-76 kcal/mol
Surface area10120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.707, 48.955, 100.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Major centromere autoantigen B / CENP-B


Mass: 7249.285 Da / Num. of mol.: 4 / Fragment: dimerization domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPB / Plasmid: pET-15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07199
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.27 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.7
Details: sodium citrate, CHES, pH 9.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 9.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
250 mMCHES1reservoirpH9.5
30.5 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9781, 0.9824, 0.9803, 0.9808
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 2, 2002
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97811
20.98241
30.98031
40.98081
ReflectionResolution: 1.65→20 Å / Num. all: 26716 / Num. obs: 23688 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.65→1.71 Å / % possible all: 78.8
Reflection
*PLUS
Redundancy: 3.1 % / Num. measured all: 73479 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 78.8 % / Rmerge(I) obs: 0.239

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→19.76 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.89 / SU B: 3.544 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30852 1188 5 %RANDOM
Rwork0.2322 ---
obs0.23596 22360 100 %-
all-22360 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.339 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2--1.18 Å20 Å2
3----0.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.65→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1547 0 0 147 1694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0211593
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.9212155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1895184
X-RAY DIFFRACTIONr_chiral_restr0.1370.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021205
X-RAY DIFFRACTIONr_nbd_refined0.2290.2803
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2122
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4480.210
X-RAY DIFFRACTIONr_mcbond_it1.2131.5944
X-RAY DIFFRACTIONr_mcangle_it2.13921539
X-RAY DIFFRACTIONr_scbond_it3.5043649
X-RAY DIFFRACTIONr_scangle_it5.2754.5616
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.651-1.6940.391630.331384
1.694-1.710.4126840.37011908
1.71-1.780.33641020.30922297
1.78-1.860.3011350.272325
1.86-1.960.3423980.33471957
1.96-2.080.25441080.24252413
2.08-2.240.21811050.23452190
2.24-2.460.21461310.24142267
2.46-2.820.21051260.21712492
2.82-3.550.21061260.22372510
3.55-200.2181280.235213842169
Software
*PLUS
Version: 5.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.309 / Rfactor Rwork: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.033
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.747

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