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- PDB-2g4s: Anomalous substructure of NBR1PB1 -

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Basic information

Entry
Database: PDB / ID: 2g4s
TitleAnomalous substructure of NBR1PB1
ComponentsNext to BRCA1 gene 1 protein
KeywordsMETAL BINDING PROTEIN / anomalous substructure of NBR1PB1
Function / homology
Function and homology information


regulation of bone mineralization / phagophore assembly site / M band / 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 / phagophore assembly site / M band / 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 gene 1 protein-like, C-terminal UBA domain / Next to BRCA1, central domain / Ig-like domain from next to BRCA1 gene / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. ...NBR1, PB1 domain / : / Next to BRCA1 gene 1 protein-like, C-terminal UBA 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 finger, ZZ type / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type 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
ACETIC ACID / Next to BRCA1 gene 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsMueller-Dieckmann, C. / Weiss, M.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths.
Authors: Mueller-Dieckmann, C. / Panjikar, S. / Schmidt, A. / Mueller, S. / Kuper, J. / Geerlof, A. / Wilmanns, M. / Singh, R.K. / Tucker, P.A. / Weiss, M.S.
History
DepositionFeb 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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

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Assembly

Deposited unit
A: Next to BRCA1 gene 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9093
Polymers9,8141
Non-polymers962
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.400, 101.400, 42.590
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 Next to BRCA1 gene 1 protein / Neighbor of BRCA1 gene 1 protein / NBR1


Mass: 9813.853 Da / Num. of mol.: 1 / Fragment: PB1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NBR1,1A13B, KIAA0049, M17S2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14596
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 3.22 Å3/Da / Density % sol: 61.8 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 7391 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
CCP4(SCALA)data scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.874 / SU B: 8.668 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32262 168 2.3 %RANDOM
Rwork0.21444 ---
obs0.21647 7223 99.85 %-
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: 51.653 Å2
Baniso -1Baniso -2Baniso -3
1--2.35 Å2-1.18 Å20 Å2
2---2.35 Å20 Å2
3---3.53 Å2
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms687 0 5 52 744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022699
X-RAY DIFFRACTIONr_bond_other_d0.0010.02605
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.952945
X-RAY DIFFRACTIONr_angle_other_deg0.79731428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.825585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.19828.15838
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51315130
X-RAY DIFFRACTIONr_chiral_restr0.0970.2107
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02782
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02113
X-RAY DIFFRACTIONr_nbd_refined0.190.2134
X-RAY DIFFRACTIONr_nbd_other0.1770.2599
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2337
X-RAY DIFFRACTIONr_nbtor_other0.0930.2443
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.232
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2870.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.27
X-RAY DIFFRACTIONr_mcbond_it1.1831.5551
X-RAY DIFFRACTIONr_mcbond_other0.1851.5175
X-RAY DIFFRACTIONr_mcangle_it1.5192.5699
X-RAY DIFFRACTIONr_scbond_it3.8335300
X-RAY DIFFRACTIONr_scangle_it5.3710246
LS refinement shellResolution: 2.15→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.609 11 -
Rwork0.189 519 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 8.846 Å / Origin y: 76.9035 Å / Origin z: 3.8092 Å
111213212223313233
T-0.1112 Å20.0391 Å20.1005 Å2--0.3288 Å20.0085 Å2---0.2414 Å2
L6.5772 °2-3.6706 °21.9775 °2-7.8619 °2-3.6095 °2--4.369 °2
S0 Å °0.2197 Å °0.577 Å °-0.6722 Å °-0.2225 Å °-0.9102 Å °0.3759 Å °0.3584 Å °0.2224 Å °

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