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- PDB-2bkf: Structure of the PB1 domain of NBR1 -

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Basic information

Entry
Database: PDB / ID: 2bkf
TitleStructure of the PB1 domain of NBR1
ComponentsZINC-FINGER PROTEIN NBR1 (NEXT TO BREAST CANCER 1)
KeywordsZINC-FINGER PROTEIN / PB1 DOMAIN / NBR1 / INTERACTION DOMAIN / ZINC-FINGER
Function / homology
Function and homology information


regulation of bone mineralization / M band / phagophore assembly site / mitogen-activated protein kinase binding / peroxisomal membrane / regulation of stress-activated MAPK cascade / negative regulation of osteoblast differentiation / autophagosome / Pexophagy / ubiquitin binding ...regulation of bone mineralization / M band / phagophore assembly site / mitogen-activated protein kinase binding / peroxisomal membrane / regulation of stress-activated MAPK cascade / negative regulation of osteoblast differentiation / autophagosome / Pexophagy / ubiquitin binding / macroautophagy / mitochondrial intermembrane space / late endosome / lysosome / receptor complex / nuclear body / intracellular membrane-bounded organelle / zinc ion binding / nucleoplasm / membrane / cytosol
Similarity search - Function
NBR1, PB1 domain / Next to BRCA1, central domain / Ig-like domain from next to BRCA1 gene / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. ...NBR1, PB1 domain / Next to BRCA1, central domain / Ig-like domain from next to BRCA1 gene / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Roll / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
Next to BRCA1 gene 1 protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.56 Å
AuthorsMueller, S. / Kursula, I. / Wilmanns, M.
CitationJournal: FEBS Lett. / Year: 2006
Title: Crystal Structure of the Pb1 Domain of Nbr1
Authors: Mueller, S. / Kursula, I. / Zou, P. / Wilmanns, M.
History
DepositionFeb 16, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ZINC-FINGER PROTEIN NBR1 (NEXT TO BREAST CANCER 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0553
Polymers9,8711
Non-polymers1842
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)100.612, 100.612, 42.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein ZINC-FINGER PROTEIN NBR1 (NEXT TO BREAST CANCER 1) / PB1 DOMAIN OF NBR1 / NEXT TO BRCA1 GENE 1 PROTEIN / 1A1-3B


Mass: 9870.903 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-85 (PB1 INTERACTION DOMAIN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14596
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.02 %
Crystal growpH: 4.1 / Details: 1.6 M AMMONIUM SULFATE,0.1 M SODIUM ACETATE PH 4.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.803
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 4, 2003 / Details: MIRROR
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.803 Å / Relative weight: 1
ReflectionResolution: 1.56→20 Å / Num. obs: 18381 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 18.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 46.6
Reflection shellResolution: 1.55→1.61 Å / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.56→21.78 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 923 5.1 %RANDOM
Rwork0.199 ---
obs0.2 17183 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0.33 Å20 Å2
2---0.66 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.56→21.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms687 0 12 94 793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022729
X-RAY DIFFRACTIONr_bond_other_d0.0010.02637
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.956985
X-RAY DIFFRACTIONr_angle_other_deg0.73431511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.665585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.81928.29341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31415140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02790
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02113
X-RAY DIFFRACTIONr_nbd_refined0.210.2140
X-RAY DIFFRACTIONr_nbd_other0.1680.2696
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2377
X-RAY DIFFRACTIONr_nbtor_other0.090.2449
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.278
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1730.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1183559
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4534716
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.614331
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5145269
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 66
Rwork0.273 1178
Refinement TLS params.Method: refined / Origin x: 8.8054 Å / Origin y: 76.3143 Å / Origin z: 3.7688 Å
111213212223313233
T-0.0513 Å20.0314 Å20.0447 Å2--0.192 Å20.0232 Å2---0.1664 Å2
L3.124 °2-2.1151 °20.9866 °2-3.5849 °2-1.6294 °2--3.4242 °2
S-0.0332 Å °0.1689 Å °0.204 Å °-0.2706 Å °-0.0793 Å °-0.3736 Å °0.2528 Å °0.3624 Å °0.1125 Å °

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