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- PDB-1k1f: Structure of the Bcr-Abl Oncoprotein Oligomerization domain -

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Basic information

Entry
Database: PDB / ID: 1k1f
TitleStructure of the Bcr-Abl Oncoprotein Oligomerization domain
ComponentsBREAKPOINT CLUSTER REGION PROTEIN
KeywordsTRANSFERASE / Oligomerization / coiled coil / Bcr-Abl kinase
Function / homology
Function and homology information


negative regulation of respiratory burst / negative regulation of cellular extravasation / negative regulation of macrophage migration / : / negative regulation of blood vessel remodeling / negative regulation of neutrophil degranulation / macrophage migration / neutrophil degranulation / intracellular protein transmembrane transport / renal system process ...negative regulation of respiratory burst / negative regulation of cellular extravasation / negative regulation of macrophage migration / : / negative regulation of blood vessel remodeling / negative regulation of neutrophil degranulation / macrophage migration / neutrophil degranulation / intracellular protein transmembrane transport / renal system process / regulation of vascular permeability / regulation of Rho protein signal transduction / focal adhesion assembly / definitive hemopoiesis / Signaling by cytosolic FGFR1 fusion mutants / activation of GTPase activity / regulation of small GTPase mediated signal transduction / inner ear morphogenesis / small GTPase-mediated signal transduction / RHOB GTPase cycle / RHOC GTPase cycle / CDC42 GTPase cycle / neuromuscular process controlling balance / homeostasis of number of cells / RHOA GTPase cycle / negative regulation of reactive oxygen species metabolic process / RAC2 GTPase cycle / RAC3 GTPase cycle / phagocytosis / positive regulation of phagocytosis / keratinocyte differentiation / RAC1 GTPase cycle / Signaling by FGFR1 in disease / GTPase activator activity / guanyl-nucleotide exchange factor activity / Schaffer collateral - CA1 synapse / brain development / modulation of chemical synaptic transmission / negative regulation of inflammatory response / actin cytoskeleton organization / protein tyrosine kinase activity / cellular response to lipopolysaccharide / dendritic spine / postsynaptic density / non-specific serine/threonine protein kinase / regulation of cell cycle / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / signal transduction / protein-containing complex / extracellular exosome / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
Bcr-Abl oncoprotein oligomerisation domain / PH domain / Bcr-Abl oncoprotein oligomerisation / Bcr-Abl oncoprotein oligomerisation domain superfamily / Bcr-Abl oncoprotein oligomerisation domain / Abr/Bcr / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Rho GTPase-activating protein domain ...Bcr-Abl oncoprotein oligomerisation domain / PH domain / Bcr-Abl oncoprotein oligomerisation / Bcr-Abl oncoprotein oligomerisation domain superfamily / Bcr-Abl oncoprotein oligomerisation domain / Abr/Bcr / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Few Secondary Structures / Irregular / PH-like domain superfamily
Similarity search - Domain/homology
Breakpoint cluster region protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsZhao, X. / Ghaffari, S. / Lodish, H. / Malashkevich, V.N. / Kim, P.S.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Structure of the Bcr-Abl oncoprotein oligomerization domain.
Authors: Zhao, X. / Ghaffari, S. / Lodish, H. / Malashkevich, V.N. / Kim, P.S.
History
DepositionSep 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BREAKPOINT CLUSTER REGION PROTEIN
B: BREAKPOINT CLUSTER REGION PROTEIN
C: BREAKPOINT CLUSTER REGION PROTEIN
D: BREAKPOINT CLUSTER REGION PROTEIN
E: BREAKPOINT CLUSTER REGION PROTEIN
F: BREAKPOINT CLUSTER REGION PROTEIN
G: BREAKPOINT CLUSTER REGION PROTEIN
H: BREAKPOINT CLUSTER REGION PROTEIN


Theoretical massNumber of molelcules
Total (without water)69,6768
Polymers69,6768
Non-polymers00
Water7,566420
1
A: BREAKPOINT CLUSTER REGION PROTEIN
B: BREAKPOINT CLUSTER REGION PROTEIN
C: BREAKPOINT CLUSTER REGION PROTEIN
D: BREAKPOINT CLUSTER REGION PROTEIN


Theoretical massNumber of molelcules
Total (without water)34,8384
Polymers34,8384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12280 Å2
ΔGint-101 kcal/mol
Surface area14780 Å2
MethodPISA
2
E: BREAKPOINT CLUSTER REGION PROTEIN
F: BREAKPOINT CLUSTER REGION PROTEIN
G: BREAKPOINT CLUSTER REGION PROTEIN
H: BREAKPOINT CLUSTER REGION PROTEIN


Theoretical massNumber of molelcules
Total (without water)34,8384
Polymers34,8384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-103 kcal/mol
Surface area14650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.988, 121.173, 60.432
Angle α, β, γ (deg.)90.00, 93.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BREAKPOINT CLUSTER REGION PROTEIN


Mass: 8709.438 Da / Num. of mol.: 8 / Fragment: bcr1-72 / Mutation: C38A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P11274, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 1.89 Å3/Da / Density % sol: 34.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlBcr1-72C38A1drop
22.5 Mammonium sulfate1reservoir
320 mMphosphate1drop
46 Mguanidine hydrochloride1droppH6.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9686,0.9789,0.9793
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 7, 2001
RadiationMonochromator: Graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96861
20.97891
30.97931
ReflectionResolution: 2.2→20 Å / Num. all: 51720 / Num. obs: 51251 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 27.1 Å2
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 99 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→10 Å / Data cutoff high absF: 1412713.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.295 2505 -RANDOM
Rwork0.262 ---
all0.27 51720 --
obs0.262 51251 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80.6333 Å2 / ksol: 0.477025 e/Å3
Displacement parametersBiso mean: 40.5 Å2
Baniso -1Baniso -2Baniso -3
1-9.21 Å20 Å20.43 Å2
2---9.68 Å20 Å2
3---0.47 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4358 0 0 420 4778
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_improper_angle_d1.06
LS refinement shellResolution: 2.4→2.55 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.308 6512 -
obs--99.9 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.06
LS refinement shell
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 2.2 Å / Rfactor Rfree: 0.387 / Rfactor Rwork: 0.308 / Rfactor obs: 0.308

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