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- PDB-4h54: Crystal structure of the diguanylate cyclase DgcZ -

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Basic information

Entry
Database: PDB / ID: 4h54
TitleCrystal structure of the diguanylate cyclase DgcZ
ComponentsDiguanylate cyclase YdeH
KeywordsTRANSFERASE / zinc sensor / c-di-GMP / CZB domain
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum assembly / positive regulation of single-species biofilm formation on inanimate substrate / negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase / diguanylate cyclase activity / cell pole / cell adhesion involved in single-species biofilm formation / metabolic process / GTP binding / protein homodimerization activity ...negative regulation of bacterial-type flagellum assembly / positive regulation of single-species biofilm formation on inanimate substrate / negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase / diguanylate cyclase activity / cell pole / cell adhesion involved in single-species biofilm formation / metabolic process / GTP binding / protein homodimerization activity / zinc ion binding / identical protein binding / plasma membrane
Similarity search - Function
Aspartate receptor, ligand-binding domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits ...Aspartate receptor, ligand-binding domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-C2E / GUANOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE / Diguanylate cyclase DgcZ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsZaehringer, F. / Schirmer, T.
CitationJournal: Structure / Year: 2013
Title: Structure and signaling mechanism of a zinc-sensory diguanylate cyclase.
Authors: Zahringer, F. / Lacanna, E. / Jenal, U. / Schirmer, T. / Boehm, A.
History
DepositionSep 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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_asym_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_asym_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_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: Diguanylate cyclase YdeH
B: Diguanylate cyclase YdeH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,79611
Polymers69,7692
Non-polymers3,0279
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-109 kcal/mol
Surface area26060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.593, 102.593, 129.156
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Diguanylate cyclase YdeH / DgcZ / DGC


Mass: 34884.426 Da / Num. of mol.: 2 / Mutation: C52A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1535, JW1528, ydeG, ydeH / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P31129, diguanylate cyclase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GAV / GUANOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: 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.: 1 / Source method: obtained synthetically / Formula: C20H24N10O14P2

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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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 200 mM calcium acetate, 20.0% PEG4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 14, 2011
RadiationMonochromator: Bartels Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.9→89 Å / Num. all: 7096 / Num. obs: 7076 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 104.93 Å2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
3.9-4.117.930.7710.83199.87
4.11-4.3612.270.571.310.59199.96
4.36-4.6614.30.41.810.42199.96
4.66-4.6614.310.312.360.32199.96
4.66-5.5214.360.262.880.27199.96
5.52-6.1714.190.252.930.26199.95
6.17-7.1214.280.174.130.17199.97
7.12-8.7214.210.079.540.07199.94
8.72-12.3313.980.0415.530.04199.92
12.33-89.0513.380.0315.450.04199.06

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
MARMOSAIC225data collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3T90 AND 3TVK

3t90

3tvk


Resolution: 3.9→73.2 Å / Cor.coef. Fo:Fc: 0.7059 / Cor.coef. Fo:Fc free: 0.6601 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.716 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 335 4.74 %RANDOM
Rwork0.2422 ---
obs0.2421 7072 99.76 %-
all-7096 --
Displacement parametersBiso mean: 68.05 Å2
Baniso -1Baniso -2Baniso -3
1--21.3747 Å20 Å20 Å2
2---21.3747 Å20 Å2
3---42.7495 Å2
Refine analyzeLuzzati coordinate error obs: 0.846 Å
Refinement stepCycle: LAST / Resolution: 3.9→73.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4348 0 162 0 4510
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0164613HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.046297HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1613SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes120HARMONIC2
X-RAY DIFFRACTIONt_gen_planes656HARMONIC5
X-RAY DIFFRACTIONt_it4613HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.69
X-RAY DIFFRACTIONt_other_torsion15.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion605SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5723SEMIHARMONIC4
LS refinement shellResolution: 3.9→4.36 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2411 102 5.12 %
Rwork0.239 1892 -
all0.2391 1994 -
obs--99.76 %
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)
122.0222.6762-0.24961.88345.60696.53770.5997-1.2916-1.69041.6391-1.1793-1.0037-0.11240.64920.5797-0.24130.58250.1972-0.1783-0.0543-0.176875.1225-28.0243-0.0934
29.5482-0.3882-0.299816.39110.104111.93670.21040.2438-0.6238-1.0938-0.16760.61091.85710.4205-0.0428-1.0546-0.8601-0.3722-0.40670.0293-1.034132.3592-41.59746.2266
330.41694.3169-0.106-5.15436.97361.62390.7992-1.1562.90132.1379-1.9526-1.1317-1.39152.31741.1535-0.46960.72010.2998-1.1023-0.0760.223769.1571-11.1277-3.932
47.06531.762-1.567215.784-0.76629.99170.227-0.2160.8827-1.57950.31850.51670.3619-1.1263-0.5455-0.2507-0.4411-0.2855-0.4045-0.2478-1.447929.9366-18.6675-9.5784
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|5 - A|35 A|54 - A|126 A|400 }A5 - 35
2X-RAY DIFFRACTION1{ A|5 - A|35 A|54 - A|126 A|400 }A54 - 126
3X-RAY DIFFRACTION1{ A|5 - A|35 A|54 - A|126 A|400 }A400 - 401
4X-RAY DIFFRACTION2{ A|127 - A|296 A|600 A|601 A|700 A|701 }A127 - 296
5X-RAY DIFFRACTION2{ A|127 - A|296 A|600 A|601 A|700 A|701 }A402 - 600
6X-RAY DIFFRACTION2{ A|127 - A|296 A|600 A|601 A|700 A|701 }A403 - 601
7X-RAY DIFFRACTION2{ A|127 - A|296 A|600 A|601 A|700 A|701 }A404 - 700
8X-RAY DIFFRACTION2{ A|127 - A|296 A|600 A|601 A|700 A|701 }A405 - 701
9X-RAY DIFFRACTION3{ B|2 - B|35 B|65 - B|126 B|400 }B2 - 35
10X-RAY DIFFRACTION3{ B|2 - B|35 B|65 - B|126 B|400 }B65 - 126
11X-RAY DIFFRACTION3{ B|2 - B|35 B|65 - B|126 B|400 }B400 - 401
12X-RAY DIFFRACTION4{ B|127 - B|296 B|600 B|601 B|700}B127 - 296
13X-RAY DIFFRACTION4{ B|127 - B|296 B|600 B|601 B|700}B402 - 600
14X-RAY DIFFRACTION4{ B|127 - B|296 B|600 B|601 B|700}B403 - 601
15X-RAY DIFFRACTION4{ B|127 - B|296 B|600 B|601 B|700}B404 - 700

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