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- PDB-2zp2: C-terminal domain of KipI from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 2zp2
TitleC-terminal domain of KipI from Bacillus subtilis
ComponentsKinase A inhibitor
KeywordsTRANSFERASE INHIBITOR / kipI / histidine kinase inhibitor / ATP-binding / Nucleotide-binding / Protein kinase inhibitor / Sporulation
Function / homology
Function and homology information


5-oxoprolinase (ATP-hydrolysing) / 5-oxoprolinase (ATP-hydrolyzing) activity / sporulation resulting in formation of a cellular spore / protein kinase inhibitor activity / ATP binding
Similarity search - Function
KipI family / Carboxyltransferase domain, subdomain C and D / Carboxyltransferase domain, subdomain C and D / Allophanate hydrolase subunit 1 / Cyclophilin-like / Cyclophilin / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
5-oxoprolinase subunit B
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsLangley, D.B. / Jacques, D.A.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Histidine kinase regulation by a cyclophilin-like inhibitor
Authors: Jacques, D.A. / Langley, D.B. / Jeffries, C.M. / Cunningham, K.A. / Burkholder, W.F. / Guss, J.M. / Trewhella, J.
History
DepositionJun 24, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinase A inhibitor
B: Kinase A inhibitor


Theoretical massNumber of molelcules
Total (without water)30,6832
Polymers30,6832
Non-polymers00
Water00
1
A: Kinase A inhibitor


Theoretical massNumber of molelcules
Total (without water)15,3421
Polymers15,3421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kinase A inhibitor


Theoretical massNumber of molelcules
Total (without water)15,3421
Polymers15,3421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.909, 84.417, 84.409
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Kinase A inhibitor / Sporulation inhibitor kipI


Mass: 15341.532 Da / Num. of mol.: 2 / Fragment: C-terminal domain, UNP residues 100-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: kipI / Plasmid: pET (novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60495

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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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 15% PEG 8000, 20% glycerol, 40mM potassium phosphate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 15, 2008 / Details: Osmic mirror optics
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→17 Å / Num. all: 6751 / Num. obs: 6738 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 78 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.7
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.5 / Num. unique all: 629 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PHC

2phc


Resolution: 3.01→16.88 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.788 / SU B: 21.564 / SU ML: 0.415 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.533 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS but are not displayed in the PDB
RfactorNum. reflection% reflectionSelection details
Rfree0.34378 321 4.8 %RANDOM
Rwork0.26354 ---
all0.26747 6399 --
obs0.26747 6375 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.673 Å2
Baniso -1Baniso -2Baniso -3
1-3.09 Å20 Å20 Å2
2---1.64 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 3.01→16.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1635 0 0 0 1635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221677
X-RAY DIFFRACTIONr_bond_other_d0.0010.021050
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.992302
X-RAY DIFFRACTIONr_angle_other_deg0.88232593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2225239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90623.7540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.44915187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.555152
X-RAY DIFFRACTIONr_chiral_restr0.0690.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021933
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02315
X-RAY DIFFRACTIONr_nbd_refined0.2140.2448
X-RAY DIFFRACTIONr_nbd_other0.1850.21067
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2827
X-RAY DIFFRACTIONr_nbtor_other0.0890.2865
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.243
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1820.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2930.23
X-RAY DIFFRACTIONr_symmetry_hbond_other0.10.21
X-RAY DIFFRACTIONr_mcbond_it1.27121221
X-RAY DIFFRACTIONr_mcbond_other0.2512494
X-RAY DIFFRACTIONr_mcangle_it2.18831882
X-RAY DIFFRACTIONr_scbond_it3.0134523
X-RAY DIFFRACTIONr_scangle_it4.4746420
LS refinement shellResolution: 3.007→3.082 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.494 19 -
Rwork0.302 424 -
obs--95.27 %

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