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- PDB-1w25: Response regulator PleD in complex with c-diGMP -

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Basic information

Entry
Database: PDB / ID: 1w25
TitleResponse regulator PleD in complex with c-diGMP
ComponentsSTALKED-CELL DIFFERENTIATION CONTROLLING PROTEIN
KeywordsSIGNALING PROTEIN / TWO-COMPONENT SYSTEM / GGDEF DOMAIN / CYCLIC DINUCLEOTIDE / CYCLIC-DIGMP / ALLOSTERIC PRODUCT INHIBITION / PHOSPHORYLATION
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
Chem-C2E / Response regulator PleD / Response regulator PleD
Similarity search - Component
Biological speciesCAULOBACTER VIBRIOIDES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsChan, C. / Schirmer, T. / Jenal, U.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structural Basis of Activity and Allosteric Control of Diguanylate Cyclase
Authors: Chan, C. / Paul, R. / Samoray, D. / Amiot, N. / Giese, B. / Jenal, U. / Schirmer, T.
History
DepositionJun 28, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 29, 2019Group: Data collection / Other / Category: pdbx_database_proc / pdbx_database_status
Item: _pdbx_database_status.date_of_sf_release / _pdbx_database_status.status_code_sf
Revision 1.4May 8, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ncs_dom_lim / 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_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_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET SHEET C OF CHAINS A AND B IS EXTENDED BY 2 ADDITIONAL SHORT BETA-STRANDS (CALLED BETA0 AND ... SHEET SHEET C OF CHAINS A AND B IS EXTENDED BY 2 ADDITIONAL SHORT BETA-STRANDS (CALLED BETA0 AND BETA0PRIME) AT THE EDGE FORMED BY STRAND 1 IN CHAIN A: IN CHAIN B: 0 VAL A 290 ASP A 292 0 VAL B 290 ASP B 292 0' LEU A 297 ASN A 299 0' LEU B 297 ASN B 299

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STALKED-CELL DIFFERENTIATION CONTROLLING PROTEIN
B: STALKED-CELL DIFFERENTIATION CONTROLLING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,34310
Polymers100,7772
Non-polymers3,5668
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-17.6 kcal/mol
Surface area42390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.870, 135.870, 169.247
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERVALVAL1AA2 - 1161 - 115
21SERSERVALVAL1BB2 - 1161 - 115
12SERSERGLUGLU2AA118 - 163117 - 162
22SERSERGLUGLU2BB118 - 163117 - 162
13GLNGLNGLNGLN3AA165 - 167164 - 166
23GLNGLNGLNGLN3BB165 - 167164 - 166
14VALVALALAALA4AA169 - 403168 - 402
24VALVALALAALA4BB169 - 403168 - 402
15GLYGLYHISHIS5AA405 - 455404 - 454
25GLYGLYHISHIS5BB405 - 455404 - 454
16MGMGMGMG6AD500
26MGMGMGMG6BH500
17C2EC2EC2EC2E1AF - G503 - 505
27C2EC2EC2EC2E1BI - J503 - 505

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Components

#1: Protein STALKED-CELL DIFFERENTIATION CONTROLLING PROTEIN / DIGUANYLATE CYCLASE


Mass: 50388.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAULOBACTER VIBRIOIDES (bacteria) / Strain: CB15 / Plasmid: PCF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: Q9A5I5, UniProt: B8GZM2*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / 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.: 5 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE N-TERMINAL REGION IS SIMILAR TO THAT OF OTHER REGULATORY COMPONENTS OF SENSORY TRANSDUCTION SYSTEMS.
Sequence detailsMET1 HAS BEEN CLEAVED OFF. 6 HISTIDINES HAVE BEEN ADDED TO THE C-TERMINUS.

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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: 3.9 Å3/Da / Density % sol: 69 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 9.2
Details: CRYSTALS WERE OBTAINED AT ROOM TEMPERATURE BY HANGING DROP VAPOUR DIFFUSION. FOR THIS, PLED AT A NOMINAL CONCENTRATION OF 10 MG/ML IN 20 MM TRIS-HCL (PH 8.0), 100 MM NACL, 1 MM DTT, 2 MM ...Details: CRYSTALS WERE OBTAINED AT ROOM TEMPERATURE BY HANGING DROP VAPOUR DIFFUSION. FOR THIS, PLED AT A NOMINAL CONCENTRATION OF 10 MG/ML IN 20 MM TRIS-HCL (PH 8.0), 100 MM NACL, 1 MM DTT, 2 MM MGCL2 AND 0.8 MM C-DIGMP6 WAS MIXED WITH THE RESERVOIR (1.0 M GLYCINE PH 9.2, 2 % DIOXANE, 14.5 % POLYETHYLENE GLYCOL 20K) AT A RATIO 1 TO 1.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlPleD1drop
220 mMTris-HCl1droppH8.0
3100 mM1dropNaCl
41 mMdithiothreitol1drop
52 mM1dropMgCl2
60.8 mMc-diGMP1drop
71.0 Mglycine1reservoirpH9.2
82 %dioxane1reservoir
914.5 %PEG200001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9795
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→60.86 Å / Num. obs: 43706 / % possible obs: 99.3 % / Observed criterion σ(I): -3.7 / Redundancy: 5.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.42
Reflection shellResolution: 2.7→2.72 Å / Redundancy: 5.48 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.96 / % possible all: 98.7
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 42707 / Redundancy: 5.7 % / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
Lowest resolution: 2.85 Å / % possible obs: 98.7 % / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
DMmodel building
TRUNCATEdata scaling
SHELXDphasing
SHARPphasing
SOLOMONphasing
DMphasing
REFMAC5.2.0001refinement
RefinementMethod to determine structure: MAD / Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.921 / SU B: 20.488 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.408 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY CONTAINS ATOMS REFINED WITH WITH AN OCCUPANCY OF 0.00.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2202 5 %RANDOM
Rwork0.21 ---
obs0.212 41469 98.9 %-
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: 25.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6962 0 233 15 7210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226974
X-RAY DIFFRACTIONr_bond_other_d0.0010.026560
X-RAY DIFFRACTIONr_angle_refined_deg1.2112.0059492
X-RAY DIFFRACTIONr_angle_other_deg0.773315110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5865866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95623.133300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4151172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9451578
X-RAY DIFFRACTIONr_chiral_restr0.0650.21112
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027668
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021402
X-RAY DIFFRACTIONr_nbd_refined0.2010.21291
X-RAY DIFFRACTIONr_nbd_other0.170.26396
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.24318
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2950.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1291.55624
X-RAY DIFFRACTIONr_mcbond_other0.181.51778
X-RAY DIFFRACTIONr_mcangle_it1.30726940
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.41633030
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7064.52552
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

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2105tight positional0.020.05
2B2105tight positional0.020.05
1A4077medium positional0.180.5
2B4077medium positional0.180.5
1A410loose positional0.325
2B410loose positional0.325
1A2105tight thermal0.050.5
2B2105tight thermal0.050.5
1A4077medium thermal0.242
2B4077medium thermal0.242
1A410loose thermal0.7310
2B410loose thermal0.7310
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.363 165
Rwork0.345 2978
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)
12.15950.1683-0.61711.625-0.21041.6217-0.0188-0.2296-0.06140.15390.01310.08290.0048-0.05880.00570.08560.03110.0052-0.0251-0.0440.3004101.99111.7655.452
22.03420.06790.25642.17320.09731.5335-0.0572-0.18310.06330.30790.0161-0.2486-0.13650.11210.04110.16050.0421-0.0459-0.03860.02660.3066100.42448.64852.774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 455
2X-RAY DIFFRACTION1A500
3X-RAY DIFFRACTION1A503 - 505
4X-RAY DIFFRACTION2B2 - 455
5X-RAY DIFFRACTION2B500
6X-RAY DIFFRACTION2B503 - 505
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.008
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.2
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.77 Å

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