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- PDB-2z13: Crystal structure of the N-terminal DUF1126 in human EF-hand domain -

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Basic information

Entry
Database: PDB / ID: 2z13
TitleCrystal structure of the N-terminal DUF1126 in human EF-hand domain
ComponentsEF-hand domain-containing family member C2
KeywordsStructural genomics / unknown function / DUF1126 / human ef-hand / Alternative splicing / Polymorphism / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


axonemal A tubule inner sheath / axonemal microtubule / regulation of neuron projection development / ciliary basal body / cellular response to leukemia inhibitory factor / calcium ion binding
Similarity search - Function
PH-domain like - #170 / DM10 domain / EF-hand domain-containing protein EFHC1/EFHC2/EFHB / DM10 domain / DM10 domain profile. / Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases. / PH-domain like / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair ...PH-domain like - #170 / DM10 domain / EF-hand domain-containing protein EFHC1/EFHC2/EFHB / DM10 domain / DM10 domain profile. / Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases. / PH-domain like / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Roll / Mainly Beta
Similarity search - Domain/homology
EF-hand domain-containing family member C2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.84 Å
AuthorsSaito, K. / Kishishita, 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 N-terminal DUF1126 in human EF-hand domain
Authors: Saito, K. / Kishishita, 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 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EF-hand domain-containing family member C2


Theoretical massNumber of molelcules
Total (without water)15,3431
Polymers15,3431
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.460, 35.280, 39.150
Angle α, β, γ (deg.)90.00, 112.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein EF-hand domain-containing family member C2


Mass: 15343.044 Da / Num. of mol.: 1 / Fragment: UNP residues 71-190 / Mutation: I118M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: EFHC2 / Plasmid: PX060518-19 / References: UniProt: Q5JST6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 1.98 Å3/Da / Density % sol: 37.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M Sodium iodate, 0.1M Bis-Tris, 20% PEG3350, pH7.0, 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: 0.9790, 0.9793, 0.964
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 10, 2006 / Details: mirrors
RadiationMonochromator: Si II / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97931
30.9641
ReflectionResolution: 1.84→50 Å / Num. obs: 10156 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3.49 % / Biso Wilson estimate: 7.6 Å2 / Rsym value: 0.037 / Net I/σ(I): 45.1
Reflection shellResolution: 1.84→1.94 Å / Mean I/σ(I) obs: 27.3 / Rsym value: 0.058 / % possible all: 95.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.84→35.41 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 346110 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 507 4.7 %RANDOM
Rwork0.181 ---
obs0.181 10156 90.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.6108 Å2 / ksol: 0.38435 e/Å3
Displacement parametersBiso mean: 14.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å21.57 Å2
2---0.79 Å20 Å2
3----0.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.84→35.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 0 172 1164
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_d26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.68→1.79 Å / Total num. of bins used: 6 /
RfactorNum. reflection
Rwork0.227 0
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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