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Basic information

Entry
Database: PDB / ID: 3gwr
TitleCrystal structure of Putative calcium/calmodulin-dependent protein kinase type II association domain (YP_315894.1) from THIOBACILLUS DENITRIFICANS ATCC 25259 at 2.00 A resolution
ComponentsPutative calcium/calmodulin-dependent protein kinase type II association domain
KeywordsPROTEIN BINDING / YP_315894.1 / Putative calcium/calmodulin-dependent protein kinase type II association domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / TRANSFERASE
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 / Unknown ligand / SnoaL-like domain-containing protein
Function and homology information
Biological speciesThiobacillus denitrificans ATCC 25259 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.01 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative calcium/calmodulin-dependent protein kinase type II association domain (YP_315894.1) from THIOBACILLUS DENITRIFICANS ATCC 25259 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 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 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
Revision 1.5Nov 27, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative calcium/calmodulin-dependent protein kinase type II association domain
B: Putative calcium/calmodulin-dependent protein kinase type II association domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,09610
Polymers31,9312
Non-polymers1,1658
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-12 kcal/mol
Surface area12240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.445, 89.655, 90.259
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUARGARGAA3 - 344 - 35
21GLUGLUARGARGBB3 - 344 - 35
12VALVALILEILEAA38 - 9439 - 95
22VALVALILEILEBB38 - 9439 - 95
13ALAALAGLNGLNAA99 - 128100 - 129
23ALAALAGLNGLNBB99 - 128100 - 129
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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


Mass: 15965.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiobacillus denitrificans ATCC 25259 (bacteria)
Gene: Tbd_2136, YP_315894.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q3SH04
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE THIS CONSTRUCT (WITH MUTATION E14D) WAS EXPRESSED WITH A PURIFICATION TAG ...SEQUENCE THIS CONSTRUCT (WITH MUTATION E14D) 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: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2000M NH4F, 20.0000% PEG-3350, No Buffer pH 6.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97966,0.97951
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 17, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979661
30.979511
ReflectionResolution: 2→28.892 Å / Num. obs: 22722 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.968 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 9.23
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.070.5861.472433711185.4
2.07-2.150.4481.880084094196.9
2.15-2.250.3542.385914346196.7
2.25-2.370.2573.184994287196.3
2.37-2.520.2193.785134266196.1
2.52-2.710.165582874116195.7
2.71-2.990.1067.687504318195.1
2.99-3.420.05713.184084140194.9
3.42-4.30.02923.683744089193.9
4.3-28.8920.02330.885254119192.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.01→28.892 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 6.881 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.138
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. PG4 MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. 5. AN UNKNOWN LIGAND (UNL) RESEMBLING BENZOIC ACID OR NITROBENZENE IS MODELED NEAR RESIDUE HIS 122 IN BOTH CHAINS. 6. LOOP REGION RESIDUES 94-98 ARE DISORDRED AND HAVE POOR DENSITY SUPPORT.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1177 5.2 %RANDOM
Rwork0.173 ---
obs0.175 22693 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 85.38 Å2 / Biso mean: 38.927 Å2 / Biso min: 20.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2---1.23 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.01→28.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 65 105 2128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222125
X-RAY DIFFRACTIONr_bond_other_d0.0020.021442
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.9492885
X-RAY DIFFRACTIONr_angle_other_deg0.92333476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7885268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.14722100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08315305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7121523
X-RAY DIFFRACTIONr_chiral_restr0.1020.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022393
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02466
X-RAY DIFFRACTIONr_nbd_refined0.2090.2383
X-RAY DIFFRACTIONr_nbd_other0.2080.21512
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2948
X-RAY DIFFRACTIONr_nbtor_other0.0850.21148
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.293
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0740.24
X-RAY DIFFRACTIONr_mcbond_it1.49621347
X-RAY DIFFRACTIONr_mcbond_other0.2772510
X-RAY DIFFRACTIONr_mcangle_it2.33742080
X-RAY DIFFRACTIONr_scbond_it3.8026893
X-RAY DIFFRACTIONr_scangle_it5.2638797
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1547 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.345
LOOSE THERMAL1.8910
LS refinement shellResolution: 2.005→2.058 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 85 -
Rwork0.232 1505 -
all-1590 -
obs--93.42 %
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)
11.0558-0.108-0.192.91561.04911.42220.066-0.23920.24270.00040.0448-0.1765-0.14710.0829-0.1107-0.0945-0.003-0.0049-0.0115-0.0747-0.047410.82240.90517.901
22.21610.5123-0.31611.575-0.06561.36570.0137-0.1769-0.0760.0079-0.01020.11710.1085-0.0481-0.0035-0.1309-0.0008-0.0063-0.08890.0012-0.1075-1.33822.40711.613
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 128
2X-RAY DIFFRACTION2B1 - 128

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