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- PDB-6pwj: Vibrio cholerae LapD S helix-GGDEF-EAL (apo) -

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Basic information

Entry
Database: PDB / ID: 6pwj
TitleVibrio cholerae LapD S helix-GGDEF-EAL (apo)
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
TRIETHYLENE GLYCOL / 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: 2.7 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 / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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 1.3Mar 13, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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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)94,8495
Polymers94,6502
Non-polymers1993
Water19811
1
A: GGDEF and EAL domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3492
Polymers47,3251
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GGDEF and EAL domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5003
Polymers47,3251
Non-polymers1742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.830, 129.830, 114.441
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.94 Å3/Da / Density % sol: 58.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.5 M sodium acetate trihydrate, pH 7.0 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.6309 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6309 Å / Relative weight: 1
ReflectionResolution: 2.7→19.534 Å / Num. obs: 29068 / % possible obs: 94.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 45.17 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.037 / Rrim(I) all: 0.102 / Net I/σ(I): 14.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.837.70.4142966638680.9220.1590.4454.795.7
8.95-19.535.70.06843477600.9910.0280.07422.983.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.5.8data scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→12.69 Å / SU ML: 0.3158 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7815
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2427 1974 6.84 %
Rwork0.1987 26871 -
obs0.2017 28845 94.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.82 Å2
Refinement stepCycle: LAST / Resolution: 2.7→12.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6486 0 12 11 6509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00136627
X-RAY DIFFRACTIONf_angle_d0.36638961
X-RAY DIFFRACTIONf_chiral_restr0.0386994
X-RAY DIFFRACTIONf_plane_restr0.00251159
X-RAY DIFFRACTIONf_dihedral_angle_d13.42723926
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.29371400.25011898X-RAY DIFFRACTION95.19
2.77-2.840.34811410.25581926X-RAY DIFFRACTION95.34
2.84-2.920.28211420.25261907X-RAY DIFFRACTION95.13
2.92-3.020.2931450.24371914X-RAY DIFFRACTION94.75
3.02-3.120.29831420.24651912X-RAY DIFFRACTION94.22
3.12-3.250.26111380.23081904X-RAY DIFFRACTION94.58
3.25-3.390.26851460.22011930X-RAY DIFFRACTION94.84
3.39-3.570.22231390.21141911X-RAY DIFFRACTION94.43
3.57-3.780.24581400.1951921X-RAY DIFFRACTION94.45
3.78-4.070.25541420.18111927X-RAY DIFFRACTION93.92
4.07-4.460.2051380.16541917X-RAY DIFFRACTION93.54
4.46-5.070.1961420.1651915X-RAY DIFFRACTION93.37
5.07-6.260.22311370.19371925X-RAY DIFFRACTION92.47
6.26-12.690.21921420.17321964X-RAY DIFFRACTION91.84
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)
13.27492232743-0.491612869045-0.3269072520211.05061292107-0.02193262527161.20317381740.2251340053250.2530852148930.387474460764-0.0981968785653-0.0511950602182-0.0148071698198-0.0220229704142-0.117292411892-0.140839035070.276034081999-0.06255185181890.06114646620240.3071628086820.03539344236630.29246754830753.719172269-47.40944347575.55506062046
22.32497471326-0.7771316002340.1601022523181.43600524470.05452525723151.167159464930.1461761811480.38548968852-0.497060135761-0.1315038910850.0225178128974-0.005554786348450.2331726429110.090826380761-0.1774217847250.319647946959-0.04660864670970.005192771984430.401954756144-0.111226944420.43108991102134.161756718-73.498400377614.0053848972
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 221:636
2X-RAY DIFFRACTION2CHAIN B AND RESID 221:636

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