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- PDB-2z0w: Crystal structure of the 2nd CAP-Gly domain in human Restin-like ... -

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Basic information

Entry
Database: PDB / ID: 2z0w
TitleCrystal structure of the 2nd CAP-Gly domain in human Restin-like protein 2 reveals a swapped-dimer
ComponentsCAP-Gly domain-containing linker protein 4
KeywordsPROTEIN BINDING / CAP-Gly domain-containing linker protein 4 / Alternative splicing / ANK repeat / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


microtubule plus-end / microtubule plus-end binding / cytoplasmic microtubule organization / intracellular membrane-bounded organelle / nucleus / cytoplasm
Similarity search - Function
CAP Gly-rich-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Domain of unknown function DUF3447 / Ankyrin repeats (3 copies) / Ankyrin repeat profile. ...CAP Gly-rich-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Domain of unknown function DUF3447 / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
CAP-Gly domain-containing linker protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsSaito, K. / Yoshikawa, S. / Nishino, A. / Murayama, K. / Terada, T. / Shirouzu, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of the 2nd CAP-Gly domain in human Restin-like protein 2 reveals a swapped-dimer
Authors: Saito, K. / Yoshikawa, S. / Nishino, A. / Murayama, K. / Terada, T. / Shirouzu, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAP-Gly domain-containing linker protein 4


Theoretical massNumber of molelcules
Total (without water)10,1961
Polymers10,1961
Non-polymers00
Water27015
1
A: CAP-Gly domain-containing linker protein 4

A: CAP-Gly domain-containing linker protein 4


Theoretical massNumber of molelcules
Total (without water)20,3922
Polymers20,3922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area3570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.173, 79.173, 62.012
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein CAP-Gly domain-containing linker protein 4 / Restin-like protein 2


Mass: 10196.236 Da / Num. of mol.: 1 / Fragment: CAP-Gly domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell Free Protein Synthesis / Plasmid: PK040816-21 / References: UniProt: Q8N3C7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.6M Li sulfate, 0.5M Ammonium Sulfate, 0.1M Na-citrate, 40% acetonitrile, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 3646 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 22.309 % / Biso Wilson estimate: 42.7 Å2 / Rsym value: 0.07 / Net I/σ(I): 52.847
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 23.4 % / Mean I/σ(I) obs: 9.668 / Num. unique all: 362 / Rsym value: 0.342 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→31.01 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 346327.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 357 10 %RANDOM
Rwork0.225 ---
obs-3574 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.2363 Å2 / ksol: 0.388256 e/Å3
Displacement parametersBiso mean: 38.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å20 Å2
2---1.21 Å20 Å2
3---2.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.5→31.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms568 0 0 15 583
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it41.5
X-RAY DIFFRACTIONc_mcangle_it4.932
X-RAY DIFFRACTIONc_scbond_it7.152
X-RAY DIFFRACTIONc_scangle_it9.072.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 58 10.2 %
Rwork0.216 508 -
obs-566 95.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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