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- PDB-2v0n: ACTIVATED RESPONSE REGULATOR PLED IN COMPLEX WITH C-DIGMP AND GTP... -

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Basic information

Entry
Database: PDB / ID: 2v0n
TitleACTIVATED RESPONSE REGULATOR PLED IN COMPLEX WITH C-DIGMP AND GTP- ALPHA-S
ComponentsRESPONSE REGULATOR PLED
KeywordsLYASE / BERYLLIUM FLUORIDE MODIFICATION / ALLOSTERIC PRODUCT INHIBITION / RESPONSE REGULATOR / CELL CYCLE / TRANSDUCER / MAGNESIUM / TWO-COMPONENT SYSTEM
Function / homology
Function and homology information


diguanylate cyclase / diguanylate cyclase activity / phosphorelay signal transduction system / cell differentiation / cell cycle / GTP binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily ...Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / Chem-C2E / GUANOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE / Response regulator PleD / Response regulator PleD
Similarity search - Component
Biological speciesCAULOBACTER VIBRIOIDES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsWassmann, P. / Schirmer, T.
CitationJournal: Structure / Year: 2007
Title: Structure of Bef3--Modified Response Regulator Pled: Implications for Diguanylate Cyclase Activation, Catalysis, and Feedback Inhibition
Authors: Wassmann, P. / Chan, C. / Paul, R. / Beck, A. / Heerklotz, H. / Jenal, U. / Schirmer, T.
History
DepositionMay 15, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Apr 3, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_biol
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / 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_database_status.status_code_sf / _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.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_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_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_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_label_seq_id / _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: RESPONSE REGULATOR PLED
B: RESPONSE REGULATOR PLED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,09818
Polymers100,7772
Non-polymers4,32116
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13930 Å2
ΔGint-87.41 kcal/mol
Surface area40540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.965, 132.557, 88.425
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A2 - 8
2111B2 - 8
1211A12 - 15
2211B12 - 15
1311A17 - 32
2311B17 - 32
1411A34 - 40
2411B34 - 40
1511A45 - 51
2511B45 - 51
1611A54 - 58
2611B54 - 58
1711A60 - 70
2711B60 - 70
1811A72 - 75
2811B72 - 75
1911A77 - 83
2911B77 - 83
11011A86 - 87
21011B86 - 87
11111A94 - 103
21111B94 - 103
11211A112 - 116
21211B112 - 116
11311A118 - 120
21311B118 - 120
11411A169 - 176
21411B169 - 176
11511A180 - 201
21511B180 - 201
11611A203 - 220
21611B203 - 220
11711A226 - 232
21711B226 - 232
11811A241 - 249
21811B241 - 249
11911A260 - 263
21911B260 - 263
12011A265 - 269
22011B265 - 269
12111A501 - 502
22111B501 - 502
1121A302 - 319
2121B302 - 319
1221A321 - 332
2221B321 - 332
1321A342 - 351
2321B342 - 351
1421A353 - 388
2421B353 - 388
1521A396 - 405
2521B396 - 405
1621A409 - 419
2621B409 - 419
1721A424 - 434
2721B424 - 434
1821A443 - 445
2821B443 - 445
1921A447 - 450
2921B447 - 450
11021A503 - 506
21021B503 - 506

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.383024, -0.920861, 0.072854), (-0.920917, 0.374507, -0.107962), (0.072134, -0.108445, -0.991482)134.58675, 100.08495, 126.97483
2given(-0.959115, -0.262122, -0.106727), (-0.261474, 0.676377, 0.688583), (-0.108306, 0.688336, -0.717261)160.52356, -14.84819, 97.72406

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein RESPONSE REGULATOR PLED / STALKED CELL DIFFERENTIATION-CONTROLLING PROTEIN / PLED


Mass: 50388.562 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-454
Source method: isolated from a genetically manipulated source
Details: BERRYLIUM FLUORIDE MODIFICATION OF A 53 AND B 53 / Source: (gene. exp.) CAULOBACTER VIBRIOIDES (bacteria) / Strain: CB15 / Plasmid: PRUN / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: Q9A5I5, UniProt: B8GZM2*PLUS, Lyases; Phosphorus-oxygen lyases

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Non-polymers , 7 types, 30 molecules

#2: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: 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.: 4 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#5: Chemical ChemComp-GAV / GUANOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.8 Å3/Da / Density % sol: 68 % / Description: NONE
Crystal growpH: 8
Details: PROTEIN SOLUTION: 100 MICROM PLED, 0.2 MM C-DI-GMP, 1 MM GTP-ALPHA-S, 1 MM BECL2, 10 MM NAF, 10 MM MGCL2 RESERVOIR: 0.1 M HEPES, PH 8.0, 0.73 M NA2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.008
DetectorType: MARRESEARCH / Detector: CCD / Date: May 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.7→73 Å / Num. obs: 39328 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 3.02 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2.58 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 6.05 / % possible all: 80.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W25

1w25


Resolution: 2.71→30 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.903 / SU B: 25.687 / SU ML: 0.231 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.54 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1969 5 %RANDOM
Rwork0.215 ---
obs0.216 37302 94 %-
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: 35.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---2.08 Å20 Å2
3---2.07 Å2
Refinement stepCycle: LAST / Resolution: 2.71→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7012 0 272 14 7298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227221
X-RAY DIFFRACTIONr_bond_other_d0.0020.024882
X-RAY DIFFRACTIONr_angle_refined_deg1.5052.0179807
X-RAY DIFFRACTIONr_angle_other_deg1.007311800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7565895
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25822.828297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.933151203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9551577
X-RAY DIFFRACTIONr_chiral_restr0.0910.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027856
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021417
X-RAY DIFFRACTIONr_nbd_refined0.2230.21465
X-RAY DIFFRACTIONr_nbd_other0.1930.24837
X-RAY DIFFRACTIONr_nbtor_refined0.1770.23516
X-RAY DIFFRACTIONr_nbtor_other0.090.24079
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0840.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2791.55819
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51527158
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.72533141
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1544.52649
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1920tight positional0.050.05
12B1920tight positional0.050.05
21A1538tight positional0.080.05
22B1538tight positional0.080.05
11A1920tight thermal0.130.5
12B1920tight thermal0.130.5
21A1538tight thermal0.150.5
22B1538tight thermal0.150.5
LS refinement shellResolution: 2.71→2.78 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.447 98
Rwork0.386 1655
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)
12.3157-0.57251.70352.1307-0.76562.455-0.048-0.17250.09190.22170.04830.0262-0.0169-0.0792-0.0003-0.06690.06040.0219-0.14720.0137-0.123394.89626.670784.5847
20.268-0.29460.17662.6018-0.48890.80870.00490.1293-0.1448-0.35040.0589-0.02780.2078-0.1732-0.0639-0.0774-0.0240.07110.073-0.02060.113780.2877-0.711271.0038
32.71730.3593-0.35482.7013-0.38762.1677-0.150.2479-0.4295-0.29760.0853-0.0910.40290.00140.0647-0.20070.0125-0.0173-0.2467-0.0406-0.239171.74751.548355.3128
41.89080.0065-1.39621.81171.1573.3811-0.01540.08010.1148-0.1034-0.02230.2807-0.1761-0.36330.0377-0.11040.03870.0481-0.0815-0.0136-0.116998.90345.254148.883
52.5749-1.471-1.93741.05751.13961.46260.037-0.30730.19270.08460.084-0.1076-0.12870.2625-0.1210.1292-0.04960.0168-0.01360.0123-0.0701109.10417.813462.7982
61.5970.8337-0.52794.3999-1.52172.70680.2334-0.3271-0.41680.6109-0.1788-0.03040.0279-0.0468-0.0546-0.0137-0.0627-0.0969-0.15040.0288-0.138872.404839.256885.717
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 131
2X-RAY DIFFRACTION1A132 - 157
3X-RAY DIFFRACTION1A501 - 502
4X-RAY DIFFRACTION2A158 - 271
5X-RAY DIFFRACTION2A272 - 299
6X-RAY DIFFRACTION3A300 - 454
7X-RAY DIFFRACTION3A503 - 506
8X-RAY DIFFRACTION3A600 - 602
9X-RAY DIFFRACTION4B2 - 131
10X-RAY DIFFRACTION4B132 - 157
11X-RAY DIFFRACTION4B501 - 502
12X-RAY DIFFRACTION5B158 - 271
13X-RAY DIFFRACTION5B272 - 299
14X-RAY DIFFRACTION6B300 - 454
15X-RAY DIFFRACTION6B503 - 506
16X-RAY DIFFRACTION6B600 - 601

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