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- PDB-3gg0: Klebsiella pneumoniae BlrP1 pH 9.0 manganese/cy-diGMP complex -

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Basic information

Entry
Database: PDB / ID: 3gg0
TitleKlebsiella pneumoniae BlrP1 pH 9.0 manganese/cy-diGMP complex
ComponentsKlebsiella pneumoniae BlrP1
KeywordsHYDROLASE / SIGNALING PROTEIN / TIM-barrel / EAL domain / BLUF domain
Function / homology
Function and homology information


blue light photoreceptor activity / FAD binding / identical protein binding / metal ion binding
Similarity search - Function
Sensors of blue-light using FAD / BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / Acylphosphatase-like domain superfamily / EAL domain ...Sensors of blue-light using FAD / BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / Acylphosphatase-like domain superfamily / EAL domain / EAL domain profile. / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-C2E / FLAVIN MONONUCLEOTIDE / : / Diguanylate phosphodiesterase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.55 Å
AuthorsBarends, T. / Hartmann, E. / Griese, J. / Beitlich, T. / Kirienko, N. / Ryjenkov, D. / Reinstein, J. / Shoeman, R. / Gomelsky, M. / Schlichting, I.
CitationJournal: Nature / Year: 2009
Title: Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase.
Authors: Barends, T.R. / Hartmann, E. / Griese, J.J. / Beitlich, T. / Kirienko, N.V. / Ryjenkov, D.A. / Reinstein, J. / Shoeman, R.L. / Gomelsky, M. / Schlichting, I.
History
DepositionFeb 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_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_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

Downloads & links

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Assembly

Deposited unit
A: Klebsiella pneumoniae BlrP1
B: Klebsiella pneumoniae BlrP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,38310
Polymers91,8702
Non-polymers2,5138
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-43 kcal/mol
Surface area33760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.020, 96.890, 126.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: FMN / End label comp-ID: FMN / Refine code: 6 / Auth seq-ID: 1 - 504 / Label seq-ID: 9

Dom-IDAuth asym-IDLabel asym-ID
1AA - F
2BB - J

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Components

#1: Protein Klebsiella pneumoniae BlrP1


Mass: 45934.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
Gene: blrp, KPN78578_15680, KPN_01598 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE-3) / References: UniProt: A6T8V8
#2: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: protein in 5 mM cy-diGMP, 5 mM CaCl2, 25 mM Tris-HCl pH 8.0, 40 mM NaCl, 5 mM MgCl2, 2 mM EDTA, 2 mM DTE, 5% glycerol, reservoir 0.1 M Na-Ac buffer pH 4.5, 0.2 M Ca-acetate, 17-20%PEG 3350, ...Details: protein in 5 mM cy-diGMP, 5 mM CaCl2, 25 mM Tris-HCl pH 8.0, 40 mM NaCl, 5 mM MgCl2, 2 mM EDTA, 2 mM DTE, 5% glycerol, reservoir 0.1 M Na-Ac buffer pH 4.5, 0.2 M Ca-acetate, 17-20%PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.2838 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2007
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2838 Å / Relative weight: 1
ReflectionResolution: 2.55→48.45 Å / Num. all: 26293 / Num. obs: 26293 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.4
Reflection shellResolution: 2.55→2.65 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 3.5 / % possible all: 84.7

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Processing

Software
NameVersionClassification
MAR345data collection
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.2.0005phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.55→48.45 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.859 / SU B: 14.756 / SU ML: 0.311 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 2.337 / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29512 1392 5 %RANDOM
Rwork0.23964 ---
all0.24245 26293 --
obs0.24245 26293 97.39 %-
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 mean: 30.994 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---4.03 Å20 Å2
3---4.06 Å2
Refinement stepCycle: LAST / Resolution: 2.55→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6169 0 158 130 6457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226476
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9862.0068820
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6555781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77222.943282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.183151066
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6881556
X-RAY DIFFRACTIONr_chiral_restr0.0440.2974
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024859
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1680.32975
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.54421
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.5410
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.352
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.58
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3851.54012
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.68826298
X-RAY DIFFRACTIONr_scbond_it0.62132868
X-RAY DIFFRACTIONr_scangle_it1.124.52520
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3135 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.665
loose thermal2.0810
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 105 -
Rwork0.332 1870 -
obs--96.58 %

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