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- PDB-2pa1: Structure of the PDZ domain of human PDLIM2 bound to a C-terminal... -

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Basic information

Entry
Database: PDB / ID: 2pa1
TitleStructure of the PDZ domain of human PDLIM2 bound to a C-terminal extension from human beta-tropomyosin
ComponentsPDZ and LIM domain protein 2
KeywordsMETAL BINDING PROTEIN / PDZ DOMAIN / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


muscle structure development / filamin binding / muscle alpha-actinin binding / cortical actin cytoskeleton / myosin heavy chain binding / filamentous actin / stress fiber / adherens junction / protein catabolic process / Z disc ...muscle structure development / filamin binding / muscle alpha-actinin binding / cortical actin cytoskeleton / myosin heavy chain binding / filamentous actin / stress fiber / adherens junction / protein catabolic process / Z disc / actin binding / heart development / actin cytoskeleton organization / ubiquitin protein ligase binding / metal ion binding / nucleus
Similarity search - Function
Domain of unknown function DUF4749 / Domain of unknown function (DUF4749) / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / Pdz3 Domain / PDZ domain ...Domain of unknown function DUF4749 / Domain of unknown function (DUF4749) / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
PDZ and LIM domain protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsUppenberg, J. / Shrestha, L. / Elkins, J. / Burgess-Brown, N. / Salah, E. / Bunkoczi, G. / Papagrigoriou, E. / Pike, A.C.W. / Turnbull, A.P. / Ugochukwu, E. ...Uppenberg, J. / Shrestha, L. / Elkins, J. / Burgess-Brown, N. / Salah, E. / Bunkoczi, G. / Papagrigoriou, E. / Pike, A.C.W. / Turnbull, A.P. / Ugochukwu, E. / Umeano, C. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Doyle, D.A. / Structural Genomics Consortium (SGC)
CitationJournal: Protein Sci. / Year: 2010
Title: Unusual binding interactions in PDZ domain crystal structures help explain binding mechanisms
Authors: Elkins, J.M. / Gileadi, C. / Shrestha, L. / Phillips, C. / Wang, J. / Muniz, J.R. / Doyle, D.A.
History
DepositionMar 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jun 23, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999SEQUENCE THESE FOUR RESIDUES BELONG TO THE C-TERMINAL EXTENSION FROM HUMAN BETA-TROPOMYOSIN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PDZ and LIM domain protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4203
Polymers9,3491
Non-polymers712
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.770, 58.770, 52.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein PDZ and LIM domain protein 2 / PDZ-LIM protein mystique / PDZ-LIM protein


Mass: 9348.724 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDLIM2, PP6345 / Plasmid: pNIC28-BSA4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96JY6
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30 % PEG Monomethylether 2000, 0.2M Ammonium sulfate, 0.1 M Sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.954 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2007
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 11401 / Num. obs: 11401 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 18.1
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 1.88 / Num. unique all: 1794 / % possible all: 98.5

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å29.39 Å
Translation2.5 Å29.39 Å

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE MODEL

Resolution: 1.7→29.39 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.262 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.104 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 544 4.8 %RANDOM
Rwork0.192 ---
all0.195 11381 --
obs0.195 11381 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.275 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å20.83 Å20 Å2
2--1.67 Å20 Å2
3----2.5 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms639 0 2 89 730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022680
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.978930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.069594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.64922.96327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71815113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.102157
X-RAY DIFFRACTIONr_chiral_restr0.0690.2107
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02527
X-RAY DIFFRACTIONr_nbd_refined0.1760.2274
X-RAY DIFFRACTIONr_nbtor_refined0.2940.2459
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.211
X-RAY DIFFRACTIONr_mcbond_it0.6011.5464
X-RAY DIFFRACTIONr_mcangle_it0.8322725
X-RAY DIFFRACTIONr_scbond_it1.4163243
X-RAY DIFFRACTIONr_scangle_it2.2294.5202
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 39 -
Rwork0.303 793 -
obs-832 98.46 %
Refinement TLS params.Method: refined / Origin x: 36.9156 Å / Origin y: 25.8897 Å / Origin z: 5.697 Å
111213212223313233
T-0.1851 Å2-0.0335 Å2-0.0377 Å2--0.0151 Å2-0.0124 Å2---0.1349 Å2
L3.4099 °20.1885 °2-0.4532 °2-2.6636 °20.9569 °2--4.5066 °2
S-0.1273 Å °0.0345 Å °0.2482 Å °-0.0027 Å °0.2046 Å °-0.2688 Å °-0.0914 Å °0.3584 Å °-0.0773 Å °
Refinement TLS groupSelection: ALL

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