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- PDB-4avm: Crystal structure of the N-BAR domain of human bridging integrator 2. -

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Basic information

Entry
Database: PDB / ID: 4avm
TitleCrystal structure of the N-BAR domain of human bridging integrator 2.
ComponentsBRIDGING INTEGRATOR 2
KeywordsPROTEIN BINDING / PLASMA MEMBRANE / BAR ADAPTOR
Function / homology
Function and homology information


plasma membrane tubulation / podosome assembly / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / podosome / anchoring junction / phagocytic cup / phagocytosis, engulfment / cell chemotaxis / cell projection / phospholipid binding ...plasma membrane tubulation / podosome assembly / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / podosome / anchoring junction / phagocytic cup / phagocytosis, engulfment / cell chemotaxis / cell projection / phospholipid binding / cell cortex / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular region / plasma membrane
Similarity search - Function
: / : / Bridging integrator 2, C-terminal / Amphiphysin / BAR domain / BAR domain profile. / BAR / Arfaptin homology (AH) domain/BAR domain / BAR domain / AH/BAR domain superfamily ...: / : / Bridging integrator 2, C-terminal / Amphiphysin / BAR domain / BAR domain profile. / BAR / Arfaptin homology (AH) domain/BAR domain / BAR domain / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bridging integrator 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsAllerston, C.K. / Krojer, T. / Cooper, C.D.O. / Vollmar, M. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Gileadi, O.
CitationJournal: To be Published
Title: Crystal Structure of the N-Bar Domain of Human Bridging Integrator 2.
Authors: Allerston, C.K. / Krojer, T. / Cooper, C.D.O. / Vollmar, M. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Gileadi, O.
History
DepositionMay 28, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Atomic model / Database references ...Atomic model / Database references / Other / Structure summary
Revision 1.2Dec 5, 2012Group: Database references / Structure summary
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _software.name / _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: BRIDGING INTEGRATOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6586
Polymers27,9961
Non-polymers6635
Water3,801211
1
A: BRIDGING INTEGRATOR 2
hetero molecules

A: BRIDGING INTEGRATOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,31712
Polymers55,9912
Non-polymers1,32610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5280 Å2
ΔGint-27.6 kcal/mol
Surface area26640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.886, 81.248, 150.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein BRIDGING INTEGRATOR 2 / BREAST CANCER-ASSOCIATED PROTEIN 1


Mass: 27995.590 Da / Num. of mol.: 1 / Fragment: N-BAR DOMAIN, RESIDUES 11-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q9UBW5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 1.95 Å3/Da / Density % sol: 36.38 % / Description: NONE
Crystal growpH: 7.5 / Details: 30% JEFFAMINE 2001, 0.1M HEPES PH 7.0, 100 MM NAI.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: MARRESEARCH MARMOSAIC 300 / Detector: CCD / Date: Apr 29, 2012 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.91→150.38 Å / Num. obs: 18417 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 22.93 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.5
Reflection shellResolution: 1.91→2.02 Å / Redundancy: 6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5.3 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
autoPROCdata reduction
AP_SCALEdata scaling
PHASERMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FIC

2fic


Resolution: 1.91→40.62 Å / Cor.coef. Fo:Fc: 0.9474 / Cor.coef. Fo:Fc free: 0.9361 / SU R Cruickshank DPI: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.158 / SU Rfree Blow DPI: 0.134 / SU Rfree Cruickshank DPI: 0.129
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 941 5.12 %RANDOM
Rwork0.1629 ---
obs0.1646 18377 99.23 %-
Displacement parametersBiso mean: 24.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.4509 Å20 Å20 Å2
2---0.1109 Å20 Å2
3---3.5618 Å2
Refine analyzeLuzzati coordinate error obs: 0.175 Å
Refinement stepCycle: LAST / Resolution: 1.91→40.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1853 0 24 211 2088
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011943HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.82619HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d951SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes63HARMONIC2
X-RAY DIFFRACTIONt_gen_planes282HARMONIC5
X-RAY DIFFRACTIONt_it1943HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion2.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion246SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies6HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2536SEMIHARMONIC4
LS refinement shellResolution: 1.91→2.03 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2347 148 5.25 %
Rwork0.1765 2672 -
all0.1797 2820 -
obs--99.23 %
Refinement TLS params.Method: refined / Origin x: -2.5892 Å / Origin y: -23.6398 Å / Origin z: -15.2463 Å
111213212223313233
T-0.0697 Å20.0089 Å20.002 Å2-0.0713 Å20.0126 Å2---0.0478 Å2
L0.1409 °20.11 °2-0.2958 °2-0.1126 °2-0.2608 °2--1.0036 °2
S-0.0024 Å °0.0017 Å °-0.0227 Å °-0.0149 Å °-0.008 Å °-0.0083 Å °0.0797 Å °0.1254 Å °0.0104 Å °
Refinement TLS groupSelection details: CHAIN A

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