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- PDB-3t9o: Regulatory CZB domain of DgcZ -

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Basic information

Entry
Database: PDB / ID: 3t9o
TitleRegulatory CZB domain of DgcZ
ComponentsDiguanylate cyclase DgcZ
KeywordsMETAL BINDING PROTEIN / diguanylate cyclase / putative zinc sensor / 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 / GTP binding / protein homodimerization activity / zinc ion binding ...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 / GTP binding / protein homodimerization activity / zinc ion binding / identical protein binding / plasma membrane
Similarity search - Function
Chemoreceptor zinc-binding domain / Chemoreceptor zinc-binding domain / Aspartate receptor, ligand-binding domain / : / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Chemoreceptor zinc-binding domain / Chemoreceptor zinc-binding domain / Aspartate receptor, ligand-binding domain / : / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Four Helix Bundle (Hemerythrin (Met), subunit A) / Reverse transcriptase/Diguanylate cyclase domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Diguanylate cyclase DgcZ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 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
DepositionAug 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Apr 27, 2016Group: Structure summary
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_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_label_asym_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 DgcZ
B: Diguanylate cyclase DgcZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5624
Polymers31,4322
Non-polymers1312
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-26 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.460, 60.260, 38.460
Angle α, β, γ (deg.)90.000, 99.040, 90.000
Int Tables number5
Space group name H-MC121
Detailsdimer

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Components

#1: Protein Diguanylate cyclase DgcZ / DGC


Mass: 15715.771 Da / Num. of mol.: 2 / Fragment: unp residues 2-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 200mM ammonium tartrate, 12.5% PEG 3350, 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: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 27377 / Num. obs: 27196 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 38.08 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 10.72
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.71 / Num. unique all: 2049 / Rsym value: 0.382 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
XDSdata scaling
autoSHARPphasing
RefinementResolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.9 / Occupancy max: 1 / Occupancy min: 0 / SU B: 12.787 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.246 698 5 %RANDOM
Rwork0.209 13274 --
obs0.211 13972 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 66.47 Å2 / Biso mean: 33.469 Å2 / Biso min: 16.24 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å20 Å20.03 Å2
2---1.31 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1837 0 2 61 1900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211897
X-RAY DIFFRACTIONr_bond_other_d0.0020.021196
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.9132573
X-RAY DIFFRACTIONr_angle_other_deg1.5213.0012903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3745225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3824.18498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61315293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.011157
X-RAY DIFFRACTIONr_chiral_restr0.0750.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022117
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02406
X-RAY DIFFRACTIONr_mcbond_it0.5781.51133
X-RAY DIFFRACTIONr_mcbond_other0.1111.5458
X-RAY DIFFRACTIONr_mcangle_it1.10221809
X-RAY DIFFRACTIONr_scbond_it1.6233764
X-RAY DIFFRACTIONr_scangle_it2.5564.5764
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 51 -
Rwork0.256 980 -
all-1031 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 24.4987 Å / Origin y: 37.0022 Å / Origin z: 8.5617 Å
111213212223313233
T0.0832 Å20.0087 Å20.012 Å2-0.0306 Å2-0.0212 Å2--0.0791 Å2
L0.816 °20.0042 °20.4005 °2-0.5372 °2-0.0408 °2--1.6811 °2
S0.0251 Å °-0.135 Å °0.0179 Å °0.087 Å °0.0369 Å °-0.0066 Å °0.0708 Å °-0.0598 Å °-0.062 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B135 - 174
2X-RAY DIFFRACTION1A135 - 155
3X-RAY DIFFRACTION1B502
4X-RAY DIFFRACTION1A502
5X-RAY DIFFRACTION1B7 - 126
6X-RAY DIFFRACTION1A5 - 126

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