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- PDB-2q3g: Structure of the PDZ domain of human PDLIM7 bound to a C-terminal... -

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Basic information

Entry
Database: PDB / ID: 2q3g
TitleStructure of the PDZ domain of human PDLIM7 bound to a C-terminal extension from human beta-tropomyosin
ComponentsPDZ and LIM domain protein 7
KeywordsSTRUCTURAL GENOMICS / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


muscle structure development / muscle alpha-actinin binding / filamentous actin / RET signaling / stress fiber / ruffle / receptor-mediated endocytosis / ossification / adherens junction / Z disc ...muscle structure development / muscle alpha-actinin binding / filamentous actin / RET signaling / stress fiber / ruffle / receptor-mediated endocytosis / ossification / adherens junction / Z disc / actin cytoskeleton / actin binding / heart development / actin cytoskeleton organization / cell differentiation / focal adhesion / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
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. ...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 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 Å
AuthorsGileadi, C. / Papagrigoriou, E. / Elkins, J. / Burgess-Brown, N. / Salah, E. / Gileadi, O. / Umeano, C. / Bunkoczi, G. / von Delft, F. / Uppenberg, J. ...Gileadi, C. / Papagrigoriou, E. / Elkins, J. / Burgess-Brown, N. / Salah, E. / Gileadi, O. / Umeano, C. / Bunkoczi, G. / von Delft, F. / Uppenberg, J. / Pike, A.C.W. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / 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
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 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 1.4Feb 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 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PDZ and LIM domain protein 7
B: PDZ and LIM domain protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8276
Polymers18,6052
Non-polymers2224
Water4,756264
1
A: PDZ and LIM domain protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3652
Polymers9,3031
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PDZ and LIM domain protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4624
Polymers9,3031
Non-polymers1603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.052, 55.404, 57.316
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe two molecules found in the asu represent two biological units

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Components

#1: Protein PDZ and LIM domain protein 7 / LIM mineralization protein / LMP / Protein enigma


Mass: 9302.571 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDLIM7 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli)
Strain (production host): BL21(DE3) with with pRARE plasmid encoding rare codon tRNAs,(chloramphenicol-resistant)
References: UniProt: Q9NR12
#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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 1.96 Å3/Da / Density % sol: 37.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES; 10% isopropanol; 20% PEG 4K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9182 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 11, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9182 Å / Relative weight: 1
ReflectionResolution: 1.11→39.84 Å / Num. all: 58681 / Num. obs: 58329 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.042 / Rsym value: 0.038
Reflection shellResolution: 1.11→1.15 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 11 / Rsym value: 0.121 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homoly based model

Resolution: 1.11→39.84 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.657 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.031 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15679 2946 5.1 %RANDOM
Rwork0.13143 ---
all0.13272 58681 --
obs0.13272 55322 99.4 %-
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: 7.247 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.11→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1405 0 13 271 1689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221455
X-RAY DIFFRACTIONr_bond_other_d0.0020.021011
X-RAY DIFFRACTIONr_angle_refined_deg1.691.9721987
X-RAY DIFFRACTIONr_angle_other_deg1.46532480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg26.9035202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65623.68457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.61815240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5791511
X-RAY DIFFRACTIONr_chiral_restr0.1130.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021661
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02289
X-RAY DIFFRACTIONr_nbd_refined0.2240.2216
X-RAY DIFFRACTIONr_nbd_other0.2080.2992
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2668
X-RAY DIFFRACTIONr_nbtor_other0.0910.2844
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2163
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2790.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.252
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6221.5975
X-RAY DIFFRACTIONr_mcbond_other0.5871.5388
X-RAY DIFFRACTIONr_mcangle_it2.24821509
X-RAY DIFFRACTIONr_scbond_it2.6673568
X-RAY DIFFRACTIONr_scangle_it3.4714.5467
X-RAY DIFFRACTIONr_rigid_bond_restr1.21132768
X-RAY DIFFRACTIONr_sphericity_free7.2143272
X-RAY DIFFRACTIONr_sphericity_bonded3.26932428
LS refinement shellResolution: 1.11→1.138 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.151 197 -
Rwork0.123 3991 -
obs--99.22 %

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