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- PDB-1wlz: Crystal structure of DJBP fragment which was obtained by limited ... -

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Basic information

Entry
Database: PDB / ID: 1wlz
TitleCrystal structure of DJBP fragment which was obtained by limited proteolysis
ComponentsCAP-binding protein complex interacting protein 1 isoform a
KeywordsUNKNOWN FUNCTION / EF-hand like
Function / homology
Function and homology information


axonemal A tubule inner sheath / flagellated sperm motility / sperm flagellum / calcium ion binding / nucleoplasm
Similarity search - Function
DJBP, EF-hand domain / EF-hand domain / : / EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...DJBP, EF-hand domain / EF-hand domain / : / EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
EF-hand calcium-binding domain-containing protein 6 / EF-hand calcium-binding domain-containing protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, SIR / Resolution: 1.6 Å
AuthorsHonbou, K. / Suzuki, N. / Horiuchi, M. / Taira, T. / Niki, T. / Ariga, H. / Inagaki, F.
CitationJournal: To be Published
Title: Crystal Structure of DJBP Fragment which was obtained by Limited Proteolysis
Authors: Honbou, K. / Suzuki, N. / Horiuchi, M. / Taira, T. / Niki, T. / Ariga, H. / Inagaki, F.
History
DepositionJul 1, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 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-binding protein complex interacting protein 1 isoform a
B: CAP-binding protein complex interacting protein 1 isoform a
C: CAP-binding protein complex interacting protein 1 isoform a
D: CAP-binding protein complex interacting protein 1 isoform a


Theoretical massNumber of molelcules
Total (without water)48,2504
Polymers48,2504
Non-polymers00
Water8,845491
1
A: CAP-binding protein complex interacting protein 1 isoform a


Theoretical massNumber of molelcules
Total (without water)12,0631
Polymers12,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CAP-binding protein complex interacting protein 1 isoform a


Theoretical massNumber of molelcules
Total (without water)12,0631
Polymers12,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CAP-binding protein complex interacting protein 1 isoform a


Theoretical massNumber of molelcules
Total (without water)12,0631
Polymers12,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CAP-binding protein complex interacting protein 1 isoform a


Theoretical massNumber of molelcules
Total (without water)12,0631
Polymers12,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.671, 68.519, 69.208
Angle α, β, γ (deg.)90.00, 102.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CAP-binding protein complex interacting protein 1 isoform a / DJBP


Mass: 12062.537 Da / Num. of mol.: 4 / Fragment: RESIDUES 229-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9H5C4, UniProt: Q5THR3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% PEG MME 2000, 0.1M Na Acetate pH 4.6, 0.2M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 30, 2002
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. all: 51566 / Num. obs: 51566 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.042
Reflection shellResolution: 1.6→1.66 Å / % possible all: 95.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD, SIR / Resolution: 1.6→19.95 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 455686.28 / 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
Rfree0.223 5082 10.1 %RANDOM
Rwork0.2 ---
obs0.2 50472 98.1 %-
all-50472 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.872 Å2 / ksol: 0.377187 e/Å3
Displacement parametersBiso mean: 17.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å20 Å20.91 Å2
2---1.26 Å20 Å2
3----1.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2709 0 0 491 3200
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.622
X-RAY DIFFRACTIONc_scbond_it1.932
X-RAY DIFFRACTIONc_scangle_it2.772.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.248 822 10.2 %
Rwork0.213 7253 -
obs--94.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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