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- PDB-2y7b: Crystal structure of the PH domain of human Actin-binding protein... -

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Basic information

Entry
Database: PDB / ID: 2y7b
TitleCrystal structure of the PH domain of human Actin-binding protein anillin ANLN
ComponentsACTIN-BINDING PROTEIN ANILLIN
KeywordsCELL CYCLE
Function / homology
Function and homology information


septin ring organization / actomyosin contractile ring assembly / positive regulation of bleb assembly / podocyte cell migration / septin ring assembly / actomyosin contractile ring / bleb / regulation of exit from mitosis / RHOB GTPase cycle / RHOC GTPase cycle ...septin ring organization / actomyosin contractile ring assembly / positive regulation of bleb assembly / podocyte cell migration / septin ring assembly / actomyosin contractile ring / bleb / regulation of exit from mitosis / RHOB GTPase cycle / RHOC GTPase cycle / mitotic cytokinesis / RHOA GTPase cycle / hematopoietic progenitor cell differentiation / actin cytoskeleton / actin binding / midbody / cell cortex / cadherin binding / nucleoplasm / cytosol
Similarity search - Function
Anillin homology domain / Anillin, N-terminal domain / Anillin, PH domain / : / Cell division protein anillin / Anillin N-terminus / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. ...Anillin homology domain / Anillin, N-terminal domain / Anillin, PH domain / : / Cell division protein anillin / Anillin N-terminus / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVollmar, M. / Wang, J. / Krojer, T. / Elkins, J. / Filippakopoulos, P. / Ugochukwu, E. / Cocking, R. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. ...Vollmar, M. / Wang, J. / Krojer, T. / Elkins, J. / Filippakopoulos, P. / Ugochukwu, E. / Cocking, R. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S.
CitationJournal: To be Published
Title: Crystal Structure of the Ph Domain of Human Actin-Binding Protein Anillin Anln
Authors: Vollmar, M. / Wang, J. / Krojer, T. / Elkins, J. / Filippakopoulos, P. / Ugochukwu, E. / Cocking, R. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S.
History
DepositionJan 31, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Structure summary / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Dec 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACTIN-BINDING PROTEIN ANILLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2166
Polymers15,9061
Non-polymers3105
Water1,40578
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.300, 59.417, 64.717
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 ACTIN-BINDING PROTEIN ANILLIN


Mass: 15905.920 Da / Num. of mol.: 1 / Fragment: PH DOMAIN, RESIDUES 980-1113
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: Q9NQW6
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.33 % / Description: NONE
Crystal growDetails: 20% PEG3350, 100 MM BIS-TRIS PH 5.5, 40% ACETONITRILE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→18.94 Å / Num. obs: 10888 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1FHW, 1U27, 1U29, 1U2B, 2R0D

1fhw

1u27

1u29

1u2b

2r0d


Resolution: 1.9→18.45 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.163 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26211 526 4.9 %RANDOM
Rwork0.19197 ---
obs0.19518 10299 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1-2.99 Å20 Å20 Å2
2---1.59 Å20 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 1.9→18.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1087 0 20 78 1185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211138
X-RAY DIFFRACTIONr_bond_other_d0.0010.02809
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9391537
X-RAY DIFFRACTIONr_angle_other_deg0.8763.0021941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66323.44361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67315197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0691514
X-RAY DIFFRACTIONr_chiral_restr0.1050.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021266
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02243
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3555677
X-RAY DIFFRACTIONr_mcbond_other1.3495271
X-RAY DIFFRACTIONr_mcangle_it4.42271097
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.0879461
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.13111437
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 42 -
Rwork0.273 727 -
obs--99.61 %
Refinement TLS params.Method: refined / Origin x: -0.7291 Å / Origin y: -3.8389 Å / Origin z: 45.6141 Å
111213212223313233
T0.0011 Å20.0021 Å20.0024 Å2-0.0698 Å20.0109 Å2--0.0448 Å2
L0.4476 °20.0334 °2-0.2551 °2-4.0578 °20.9897 °2--2.0411 °2
S-0.0049 Å °-0.0327 Å °-0.041 Å °0.061 Å °-0.0236 Å °0.1278 Å °0.0223 Å °-0.0658 Å °0.0285 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A980 - 1113
2X-RAY DIFFRACTION1A2000 - 2002
3X-RAY DIFFRACTION1A2004 - 2005

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