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- PDB-3ksp: Crystal structure of a putative ca/calmodulin-dependent kinase ii... -

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Basic information

Entry
Database: PDB / ID: 3ksp
TitleCrystal structure of a putative ca/calmodulin-dependent kinase ii association domain (exig_1688) from exiguobacterium sibiricum 255-15 at 2.59 A resolution
ComponentsCalcium/calmodulin-dependent kinase II association domain
KeywordsUNKNOWN FUNCTION / Cystatin-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologySnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / SnoaL-like domain-containing protein
Function and homology information
Biological speciesExiguobacterium sibiricum 255-15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.59 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Calcium/calmodulin-dependent kinase II association domain (YP_001814158.1) from EXIGUOBACTERIUM SP. 255-15 at 2.59 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Calcium/calmodulin-dependent kinase II association domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6733
Polymers15,4031
Non-polymers2692
Water1448
1
A: Calcium/calmodulin-dependent kinase II association domain
hetero molecules

A: Calcium/calmodulin-dependent kinase II association domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3456
Polymers30,8062
Non-polymers5394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
Buried area2650 Å2
ΔGint0 kcal/mol
Surface area13630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.226, 76.226, 144.157
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Calcium/calmodulin-dependent kinase II association domain


Mass: 15403.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exiguobacterium sibiricum 255-15 (bacteria)
Strain: DSM 17290 / JCM 13490 / 255-15 / Gene: Exig_1688 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: B1YH80
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 3.92 Å3/Da / Density % sol: 68.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 1.0000M sodium citrate, 0.1M CHES pH 9.5, 0.001 M Adenosine-5'-triphosphate (ATP), NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162,0.97929
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 8, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979291
ReflectionResolution: 2.59→28.831 Å / Num. obs: 8247 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 76.251 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 17.17
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.6-2.690.6582.253521397199.9
2.69-2.80.4153.357521493199.6
2.8-2.930.3034.557701494199.7
2.93-3.080.2166.254571409199.4
3.08-3.270.11910.655631440199.8
3.27-3.520.07116.955571439199.6
3.52-3.880.04523.757161495199.4
3.88-4.430.03430.954521429199
4.43-5.570.0335.955531460199.3
5.57-28.8310.02736.756401488198.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.59→28.831 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.22 / SU B: 19.846 / SU ML: 0.194 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.235
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 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. ETHYLENE GLYCOL (EDO) AND CHES (NHE) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 379 4.6 %RANDOM
Rwork0.201 ---
obs0.202 8207 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 83.75 Å2 / Biso mean: 44.582 Å2 / Biso min: 21.07 Å2
Baniso -1Baniso -2Baniso -3
1--2.81 Å2-1.4 Å20 Å2
2---2.81 Å20 Å2
3---4.21 Å2
Refinement stepCycle: LAST / Resolution: 2.59→28.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 17 8 1086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211138
X-RAY DIFFRACTIONr_bond_other_d0.0010.02763
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9251547
X-RAY DIFFRACTIONr_angle_other_deg0.8731849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8785136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.0424.21964
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10115183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.794156
X-RAY DIFFRACTIONr_chiral_restr0.0860.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02248
X-RAY DIFFRACTIONr_mcbond_it0.5061.5656
X-RAY DIFFRACTIONr_mcbond_other0.0881.5265
X-RAY DIFFRACTIONr_mcangle_it0.97621058
X-RAY DIFFRACTIONr_scbond_it1.6843482
X-RAY DIFFRACTIONr_scangle_it2.5464.5485
LS refinement shellResolution: 2.59→2.657 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 30 -
Rwork0.31 547 -
all-577 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 2.198 Å / Origin y: 32.054 Å / Origin z: 63.978 Å
111213212223313233
T0.2909 Å20.0887 Å20.0837 Å2-0.3623 Å20.174 Å2--0.429 Å2
L6.5398 °20.6614 °20.0759 °2-3.2542 °2-1.4297 °2--2.9774 °2
S-0.2038 Å °-0.2094 Å °-1.0536 Å °-0.2472 Å °-0.2202 Å °-0.4432 Å °0.304 Å °0.4732 Å °0.4241 Å °

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