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- PDB-6pwk: Vibrio cholerae LapD S helix-GGDEF-EAL (bound to c-di-GMP) -

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Basic information

Entry
Database: PDB / ID: 6pwk
TitleVibrio cholerae LapD S helix-GGDEF-EAL (bound to c-di-GMP)
ComponentsGGDEF and EAL domain-containing protein
KeywordsSIGNALING PROTEIN / biofilm formation / cell adhesion / c-di-GMP signaling / receptor
Function / homology
Function and homology information


membrane => GO:0016020 / signal transduction / membrane
Similarity search - Function
LapD/MoxY periplasmic domain, C-terminal / LapD/MoxY, periplasmic domain / LapD/MoxY periplasmic domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase ...LapD/MoxY periplasmic domain, C-terminal / LapD/MoxY, periplasmic domain / LapD/MoxY periplasmic domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / HAMP domain profile. / HAMP domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
Chem-C2E / Diguanylate cyclase / GGDEF and EAL domain-containing protein
Similarity search - Component
Biological speciesVibrio cholerae O1 str. 2010EL-1786 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsGiglio, K.M. / Cooley, R.B. / Sondermann, H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM123609 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103485 United States
National Science Foundation (NSF, United States)DMR-1332208 United States
CitationJournal: Mbio / Year: 2019
Title: A Conserved Regulatory Circuit Controls Large Adhesins in Vibrio cholerae.
Authors: Kitts, G. / Giglio, K.M. / Zamorano-Sanchez, D. / Park, J.H. / Townsley, L. / Cooley, R.B. / Wucher, B.R. / Klose, K.E. / Nadell, C.D. / Yildiz, F.H. / Sondermann, H.
History
DepositionJul 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 22, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GGDEF and EAL domain-containing protein
B: GGDEF and EAL domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4618
Polymers94,6502
Non-polymers2,8106
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-24 kcal/mol
Surface area36720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.379, 90.221, 82.750
Angle α, β, γ (deg.)90.000, 115.490, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein GGDEF and EAL domain-containing protein


Mass: 47325.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 str. 2010EL-1786 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H6T0A6, UniProt: A0A0H3AFX3*PLUS
#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.: 4 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M sodium formate, 0.1M bicine, pH 8.5; 20% w/v PEG MME 5000, and 0.5-1 mM c-di-GMP, 20% xylitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 31030 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 69.27 Å2 / Rmerge(I) obs: 0.062 / Χ2: 1.005 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.64-2.733.80.6631020.8791100
2.73-2.843.80.43730750.8761100
2.84-2.973.80.31230930.9621100
2.97-3.133.80.20630681.0321100
3.13-3.333.80.13931121.0561100
3.33-3.583.80.09430971.0421100
3.58-3.943.80.06730851.06199.9
3.94-4.513.80.05431081.057199.8
4.51-5.693.80.04731121.0051100
5.69-503.70.03931781.079199.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3pjx

3pjx


Resolution: 2.61→33.77 Å / SU ML: 0.413 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2241 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2485 1999 6.45 %
Rwork0.1973 28984 -
obs0.2005 30983 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.02 Å2
Refinement stepCycle: LAST / Resolution: 2.61→33.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6425 0 186 40 6651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00226765
X-RAY DIFFRACTIONf_angle_d0.66189213
X-RAY DIFFRACTIONf_chiral_restr0.04341027
X-RAY DIFFRACTIONf_plane_restr0.00261159
X-RAY DIFFRACTIONf_dihedral_angle_d16.72633898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.670.38771220.3111695X-RAY DIFFRACTION81.01
2.67-2.750.36051390.27942058X-RAY DIFFRACTION99.91
2.75-2.830.31321480.26352117X-RAY DIFFRACTION99.87
2.83-2.920.30511370.25962067X-RAY DIFFRACTION99.82
2.92-3.020.32381500.23952076X-RAY DIFFRACTION99.96
3.02-3.140.32041360.25272117X-RAY DIFFRACTION99.87
3.14-3.290.32841460.25142081X-RAY DIFFRACTION99.91
3.29-3.460.31931440.22552109X-RAY DIFFRACTION100
3.46-3.670.26161470.20492086X-RAY DIFFRACTION99.96
3.67-3.960.21291510.19142102X-RAY DIFFRACTION99.91
3.96-4.360.22311340.1732104X-RAY DIFFRACTION99.82
4.36-4.980.22211470.16472108X-RAY DIFFRACTION99.91
4.98-6.270.23621490.20232103X-RAY DIFFRACTION100
6.27-33.770.20041490.16022161X-RAY DIFFRACTION99.74
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)
14.544174135781.35168224335-1.47723634042.49232619943-1.007459583763.798455960910.0710506490375-0.382059014909-0.5302737301210.155365886326-0.251240626815-0.1894372710730.4139137154240.6316259946420.1907882764520.660621764260.124642396482-0.02288922503940.5903058814740.08261336596820.588810284631-36.9314213752-0.9296663174751.04214806107
23.610306949470.299466949959-0.04897487347032.354692196940.6913150005362.34573235701-0.01569097287120.747065643479-0.205247862172-0.288836573282-0.05784084304290.01560431751330.2926966946340.1594237415170.07131428846430.4388918071180.05086170174980.01119245442550.586600382586-0.04551585292540.434208441987-34.916897019410.4184243568-29.1618343004
36.2403213597-0.5611041565521.495075915550.7768227223720.4898414683083.10594550690.0693128535642-0.5531331211340.3623702759420.104790363469-0.02085383202-0.127749969486-0.215334501693-0.165009077322-0.041300780080.676309894522-0.01203585151440.0718578493830.4958733245210.02718543965920.517641506373-67.606682321612.11617166166.9132340695
44.26147935802-0.5869304226040.3893302626042.367828642490.05412553917721.88010710661-0.009799337053850.530611092626-0.0196013918318-0.1000830992-0.0181819926153-0.03084307807020.0810806705312-0.009828576474660.01299280865550.417229334781-0.0554010963683-0.0292212867530.507350695736-0.036138653520.467479827871-75.759451151714.128718606-24.3238480158
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 222:401
2X-RAY DIFFRACTION2CHAIN A AND RESID 402:635
3X-RAY DIFFRACTION3CHAIN B AND RESID 222:395
4X-RAY DIFFRACTION4CHAIN B AND RESID 396:635

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