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- PDB-2eaq: Crystal structure of PDZ domain of KIAA0858 (LIM), MS0793 from Ho... -

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Basic information

Entry
Database: PDB / ID: 2eaq
TitleCrystal structure of PDZ domain of KIAA0858 (LIM), MS0793 from Homo sapiens
ComponentsLIM domain only protein 7
KeywordsMETAL BINDING PROTEIN / conserved hypothetical protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of signaling / regulation of cell adhesion / ubiquitin ligase complex / post-translational protein modification / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / nuclear envelope / Neddylation / protein ubiquitination ...regulation of signaling / regulation of cell adhesion / ubiquitin ligase complex / post-translational protein modification / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / nuclear envelope / Neddylation / protein ubiquitination / apical plasma membrane / focal adhesion / cell surface / positive regulation of transcription by RNA polymerase II / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
LIM domain only protein 7 / Domain of unknown function DUF4757 / Domain of unknown function (DUF4757) / Smooth muscle protein/calponin / 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. / Calponin homology domain ...LIM domain only protein 7 / Domain of unknown function DUF4757 / Domain of unknown function (DUF4757) / Smooth muscle protein/calponin / 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. / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) 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
NICKEL (II) ION / LIM domain only protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.46 Å
AuthorsXie, Y. / Kishishita, S. / Murayama, K. / Takemoto, C. / Shirozu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of PDZ domain of KIAA0858 (LIM), MS0793 from Homo sapiens
Authors: Xie, Y. / Kishishita, S. / Murayama, K. / Takemoto, C. / Shirozu, M. / Yokoyama, S.
History
DepositionJan 31, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: LIM domain only protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2753
Polymers10,1571
Non-polymers1172
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.996, 61.311, 27.931
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2126-

NI

Detailsin this crystal packing, it looks like mononer. But, there is no experimental evidence.

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Components

#1: Protein LIM domain only protein 7 / LOMP / F-box only protein 20


Mass: 10157.312 Da / Num. of mol.: 1 / Fragment: PDZ domain, residues 1037-1126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell free / Gene: LMO7, FBX20, FBXO20, KIAA0858 / Plasmid: PK060110-33-MD01 / References: UniProt: Q8WWI1
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.85 Å3/Da / Density % sol: 33.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12% (v/v) PEG3350, HEPES-Na (pH7.5), 10mM NiSO4., VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9794, 0.9796, 0.9644
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2006 / Details: Mirrors
RadiationMonochromator: silikon / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
30.96441
ReflectionResolution: 1.46→50 Å / Num. obs: 13707 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Biso Wilson estimate: 11.5 Å2 / Rsym value: 0.079 / Net I/σ(I): 30.94
Reflection shellResolution: 1.46→1.53 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 8.28 / Num. unique all: 1661 / Rsym value: 0.298 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.46→27.93 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 245054.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1325 10.3 %RANDOM
Rwork0.16 ---
obs0.16 12910 94.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.9231 Å2 / ksol: 0.392878 e/Å3
Displacement parametersBiso mean: 13.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---1.31 Å20 Å2
3---1.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.12 Å
Luzzati d res low-5 Å
Luzzati sigma a0.04 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.46→27.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms705 0 2 137 844
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.039
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.4
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it2.622
X-RAY DIFFRACTIONc_scangle_it3.792.5
LS refinement shellResolution: 1.46→1.55 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.19 217 11.7 %
Rwork0.158 1636 -
obs--83.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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