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- PDB-3h51: Crystal structure of Putative calcium/calmodulin dependent protei... -

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Basic information

Entry
Database: PDB / ID: 3h51
TitleCrystal structure of Putative calcium/calmodulin dependent protein kinase II association domain (NP_636218.1) from XANTHOMONAS CAMPESTRIS at 1.70 A resolution
ComponentsPutative calcium/calmodulin dependent protein kinase II association domain
KeywordsPROTEIN BINDING / NP_636218.1 / Putative calcium/calmodulin dependent protein kinase II association domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / unknown function
Function / homology
Function and homology information


calmodulin-dependent protein kinase activity / calmodulin binding
Similarity search - Function
Uncharacterised conserved protein UCP028470, steroid isomerase-related / Steroid delta5-4-isomerase / Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Unknown ligand / CaMKII_AD domain-containing protein
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative calcium/calmodulin dependent protein kinase II association domain (NP_636218.1) from XANTHOMONAS CAMPESTRIS at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 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_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_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: Putative calcium/calmodulin dependent protein kinase II association domain
B: Putative calcium/calmodulin dependent protein kinase II association domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9247
Polymers34,5182
Non-polymers4065
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-5 kcal/mol
Surface area12740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.832, 80.550, 51.431
Angle α, β, γ (deg.)90.00, 95.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A24 - 160
2116B24 - 160
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Putative calcium/calmodulin dependent protein kinase II association domain


Mass: 17258.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Gene: NP_636218.1, XCC0827 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8PCA7
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 20-174) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 20-174) 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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20.0000% PEG-1000, 0.1M TRIS pH 8.5, 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: 0.91837,0.97901
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 18, 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
10.918371
20.979011
ReflectionResolution: 1.7→29.488 Å / Num. obs: 33865 / % possible obs: 97.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 22.186 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 6.464
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.743.20.6651.2790624960.66597.3
1.74-1.793.20.5251.5758623980.52597.4
1.79-1.843.20.3722.1747523550.37296.5
1.84-1.93.20.2782.8722822850.27898.5
1.9-1.963.20.2313.1702222130.23196.9
1.96-2.033.20.1884684621580.18897.4
2.03-2.113.20.1584.7657420850.15898.6
2.11-2.193.20.1355.3631419900.13597.6
2.19-2.293.20.1135.5610619310.11397.4
2.29-2.43.10.0986.6583118540.09898.8
2.4-2.533.20.0857.8560317600.08598.6
2.53-2.693.20.0768.7525316620.07698.3
2.69-2.873.20.079.1498315700.0798.3
2.87-3.13.20.0669.4456614430.06698.6
3.1-3.43.10.05511.7430013670.05598.8
3.4-3.83.10.04712.7380212080.04798.7
3.8-4.393.10.04413.1342710880.04498.2
4.39-5.383.10.04911.928379100.04999.1
5.38-7.63.10.05610.521997130.05698.2
7.6-29.493.10.04713.311573790.04794.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.488 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 4.425 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.107
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. PEG AND PG4 MOLECULES (FRAGMENTS OF PEG1000 AND PEG200) USED IN THE CRYSTALLIZATION AND CRYOPROTECTION CONDITION HAVE BEEN MODELED. 5. ELECTRON DENSITIES OF RESIDUES OF 30-34 AND 108-112 IN BOTH A AND B CHAINS ARE POOR AND MODELS ARE NOT RELIABLE IN THIS REGION. 6. AN UNIDENTIFIED LIGAND (UNL) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE OF BOTH A AND B CHAINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1695 5 %RANDOM
Rwork0.179 ---
obs0.18 33842 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.5 Å2 / Biso mean: 25.146 Å2 / Biso min: 9.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20.97 Å2
2---0.11 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2187 0 33 251 2471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222418
X-RAY DIFFRACTIONr_bond_other_d0.0020.021592
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.9573306
X-RAY DIFFRACTIONr_angle_other_deg0.9833886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0565313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42123.981108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03115383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0051514
X-RAY DIFFRACTIONr_chiral_restr0.0970.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022783
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02499
X-RAY DIFFRACTIONr_nbd_refined0.260.2472
X-RAY DIFFRACTIONr_nbd_other0.2120.21724
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21157
X-RAY DIFFRACTIONr_nbtor_other0.0880.21248
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2207
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0310.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.40.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.212
X-RAY DIFFRACTIONr_mcbond_it2.20231619
X-RAY DIFFRACTIONr_mcbond_other0.5783599
X-RAY DIFFRACTIONr_mcangle_it3.02952446
X-RAY DIFFRACTIONr_scbond_it4.99381018
X-RAY DIFFRACTIONr_scangle_it6.29111860
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1688 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.335
LOOSE THERMAL2.9210
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 137 -
Rwork0.267 2358 -
all-2495 -
obs--97.2 %
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)
11.91180.253-1.18470.9266-0.73483.0550.11840.24970.1333-0.14180.12550.1253-0.1715-0.2101-0.2439-0.04220.0044-0.0031-0.04730.02-0.042236.93765.08063.7603
21.0732-0.5135-0.76930.77760.06962.41750.08-0.19410.00790.08320.0189-0.0292-0.08010.2807-0.0989-0.0659-0.0383-0.0147-0.0131-0.0356-0.049545.64570.112622.1165
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 162
2X-RAY DIFFRACTION2B22 - 161

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