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- PDB-5jda: Bacillus cereus CotH kinase plus Mg2+/AMP -

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Basic information

Entry
Database: PDB / ID: 5jda
TitleBacillus cereus CotH kinase plus Mg2+/AMP
ComponentsSpore coat protein H
KeywordsTRANSFERASE / atypical kinase fold
Function / homologySpore coat protein CotH/Invasin CotH2/3/7 / CotH kinase protein / nucleotide binding / metal ion binding / ADENOSINE MONOPHOSPHATE / SUCCINIC ACID / Spore coat protein H
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.401 Å
AuthorsTomchick, D.R. / Tagliabracci, V.S. / Sreelatha, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Phosphorylation of spore coat proteins by a family of atypical protein kinases.
Authors: Nguyen, K.B. / Sreelatha, A. / Durrant, E.S. / Lopez-Garrido, J. / Muszewska, A. / Dudkiewicz, M. / Grynberg, M. / Yee, S. / Pogliano, K. / Tomchick, D.R. / Pawowski, K. / Dixon, J.E. / Tagliabracci, V.S.
History
DepositionApr 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jul 6, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spore coat protein H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,89819
Polymers42,6671
Non-polymers1,23118
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.757, 63.516, 118.284
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Spore coat protein H


Mass: 42667.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ATCC 10987 / NRS 248) (bacteria)
Strain: ATCC 10987 / NRS 248 / Gene: cotH, BCE_2115 / Plasmid: ppSumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q739M5, non-specific serine/threonine protein kinase

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Non-polymers , 6 types, 276 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.32 Å3/Da / Density % sol: 47.04 % / Mosaicity: 0.307 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.75
Details: 0.1 M cacodylate, 0.2 M magnesium chloride, 5 mM ADP, 15% PEG 3350, 30% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2015 / Details: monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 74634 / % possible obs: 94.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.032 / Rrim(I) all: 0.073 / Χ2: 1.495 / Net I/av σ(I): 26.093 / Net I/σ(I): 9 / Num. measured all: 344375
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.4-1.423.10.81171.2
1.42-1.453.20.725176.8
1.45-1.483.50.693181.4
1.48-1.513.70.631189.1
1.51-1.5440.591194.5
1.54-1.584.30.565197.6
1.58-1.624.60.505198.6
1.62-1.664.80.432198.7
1.66-1.714.90.36198.7
1.71-1.764.90.289198.9
1.76-1.8350.223199.4
1.83-1.950.171199.5
1.9-1.995.10.128199.2
1.99-2.095.10.104199.7
2.09-2.225.10.09199.6
2.22-2.3950.079199.7
2.39-2.6350.068199.6
2.63-3.024.90.051198.9
3.02-3.850.038198
3.8-5050.033194

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5JD9

5jd9


Resolution: 1.401→28.279 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.19
RfactorNum. reflection% reflectionSelection details
Rfree0.184 2000 2.68 %random
Rwork0.1702 ---
obs0.1706 74575 94.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.98 Å2 / Biso mean: 25.0858 Å2 / Biso min: 10.5 Å2
Refinement stepCycle: final / Resolution: 1.401→28.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3016 0 153 258 3427
Biso mean--37.67 27.29 -
Num. residues----359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0213232
X-RAY DIFFRACTIONf_angle_d0.7754316
X-RAY DIFFRACTIONf_chiral_restr0.07439
X-RAY DIFFRACTIONf_plane_restr0.004558
X-RAY DIFFRACTIONf_dihedral_angle_d15.1091214
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4008-1.43580.39391030.34673732383570
1.4358-1.47460.38261210.31654376449780
1.4746-1.5180.34121330.29764815494889
1.518-1.5670.29461430.27495214535796
1.567-1.6230.27991480.2445353550198
1.623-1.6880.24171470.21585365551299
1.688-1.76480.18981490.19255406555599
1.7648-1.85780.1971490.174253895538100
1.8578-1.97420.17551500.16155439558999
1.9742-2.12660.15991500.14995453560399
2.1266-2.34050.15781510.146854635614100
2.3405-2.67890.15321520.152255215673100
2.6789-3.37430.15641510.16075500565199
3.3743-28.28520.17321530.14955549570296
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)
10.31870.05330.06390.32720.21430.29810.04410.03440.039-0.0260.046-0.02810.03130.11190.00730.10060.00690.00860.1739-0.02440.152239.218567.410951.8028
20.44120.18190.13560.6170.78780.68260.06310.01740.00480.17990.0167-0.06510.21250.0280.05860.17140.0132-0.00730.1107-0.00150.122226.900349.931241.3131
30.66910.24050.16490.25260.55780.58190.0468-0.01970.1130.1564-0.18340.13540.1913-0.2089-0.02820.1675-0.05720.04650.1767-0.02480.157910.7956.800845.4241
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 76 )A0 - 76
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 254 )A77 - 254
3X-RAY DIFFRACTION3chain 'A' and (resid 255 through 358 )A255 - 358

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