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- PDB-5d67: Crystal structure of an EF-Hand calcium binding domain of CAP-Bin... -

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Basic information

Entry
Database: PDB / ID: 5d67
TitleCrystal structure of an EF-Hand calcium binding domain of CAP-Binding Protein Complex-Interacting Protein 1 (EFCAB6) from Homo sapiens at 2.00 A resolution
ComponentsEF-hand calcium-binding domain-containing protein 6
KeywordsMETAL BINDING PROTEIN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for Nuclear Receptor Signaling Code Biology / NHRS
Function / homology
Function and homology information


cell projection / cytoskeleton / calcium ion binding / nucleoplasm / cytoplasm
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. / EF-hand calcium-binding domain profile. ...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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for Nuclear Receptor Signaling Code Biology / Partnership for Nuclear Receptor Signaling Code Biology (NHRS)
CitationJournal: To be published
Title: Crystal structure of an EF-Hand calcium binding domain of CAP-Binding Protein Complex-Interacting Protein 1 (EFCAB6) from Homo sapiens at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for Nuclear Receptor Signaling Code Biology
History
DepositionAug 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Category: 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

Downloads & links

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Assembly

Deposited unit
A: EF-hand calcium-binding domain-containing protein 6
B: EF-hand calcium-binding domain-containing protein 6
C: EF-hand calcium-binding domain-containing protein 6
D: EF-hand calcium-binding domain-containing protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,55619
Polymers47,1154
Non-polymers1,44115
Water5,909328
1
A: EF-hand calcium-binding domain-containing protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1635
Polymers11,7791
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EF-hand calcium-binding domain-containing protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1635
Polymers11,7791
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: EF-hand calcium-binding domain-containing protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9713
Polymers11,7791
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: EF-hand calcium-binding domain-containing protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2596
Polymers11,7791
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.407, 67.187, 70.697
Angle α, β, γ (deg.)90.000, 100.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
EF-hand calcium-binding domain-containing protein 6 / CAP-binding protein complex-interacting protein 1 / DJ-1-binding protein / DJBP


Mass: 11778.729 Da / Num. of mol.: 4 / Fragment: UNP residues 1160-1260 / Mutation: D1218G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EFCAB6, DJBP, KIAA1672 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q5THR3
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.15 Å3/Da / Density % sol: 42.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 30% polyethylene glycol 4000, 0.2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97917 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 8, 2015
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2→27.118 Å / Num. obs: 26723 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.787 % / Biso Wilson estimate: 26.457 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.112 / Rrim(I) all: 0.13 / Net I/σ(I): 10.59 / Num. measured all: 197737
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
2-2.070.4730.8691.313254527444461.064184.3
2.07-2.150.6610.677217955509149770.79697.8
2.15-2.250.8090.5092.821166546554630.591100
2.25-2.370.8790.4113.520970541154020.47899.8
2.37-2.520.9110.3254.520814534453420.377100
2.52-2.710.9540.236.320441525052420.26699.8
2.71-2.990.9770.1549.121171544054270.17999.8
2.99-3.420.9930.08415.720568527852770.097100
3.42-4.30.9980.04526.620585528652870.052100
4.30.9990.03632.220813537853480.04199.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
XDSdata scaling
XSCALEdata scaling
SHELXphasing
SHARPphasing
BUSTER2.10.2refinement
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2→27.118 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.9373 / Occupancy max: 1 / Occupancy min: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE ...Details: 1. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. THE SAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 1330 4.98 %RANDOM
Rwork0.1686 ---
obs0.1704 26704 98.32 %-
Displacement parametersBiso max: 161.22 Å2 / Biso mean: 35.3461 Å2 / Biso min: 10.12 Å2
Baniso -1Baniso -2Baniso -3
1--2.9969 Å20 Å20.4464 Å2
2--0.8019 Å20 Å2
3---2.195 Å2
Refine analyzeLuzzati coordinate error obs: 0.209 Å
Refinement stepCycle: LAST / Resolution: 2→27.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2863 0 75 328 3266
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1438SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes452HARMONIC5
X-RAY DIFFRACTIONt_it3046HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion397SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3757SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3046HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4126HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion2.64
LS refinement shellResolution: 2→2.08 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2272 127 4.83 %
Rwork0.2045 2505 -
all0.2056 2632 -
obs--98.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.66050.09921.34231.6938-0.36852.681-0.02710.1052-0.0658-0.02940.0006-0.040.12290.18650.0265-0.00280.02050.0046-0.0682-0.0046-0.056618.034226.59120.0884
22.9854-0.7637-0.112.475-0.20730.97350.09010.00930.01950.043-0.12150.0547-0.0469-0.10020.03140.0057-0.00760.0144-0.0513-0.0103-0.06365.547814.281536.5491
32.03271.08440.18572.31270.22532.6163-0.1196-0.03560.0846-0.25990.09980.2108-0.0888-0.07210.01980.0159-0.0312-0.0237-0.09090.0145-0.070926.29226.368155.5346
43.399-0.8715-0.73482.14050.68781.258-0.00050.09720.1212-0.09280.0516-0.2516-0.03620.0928-0.0511-0.02-0.0087-0.0081-0.07-0.0015-0.03920.284540.02267.6047
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|0 - 1092}A0 - 1092
2X-RAY DIFFRACTION2{B|0 - 1091}B0 - 1091
3X-RAY DIFFRACTION3{C|0 - 1091}C0 - 1091
4X-RAY DIFFRACTION4{D|1010 - 1104}D1010 - 1104

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