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- PDB-3pjv: Structure of Pseudomonas fluorescence LapD periplasmic domain -

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Basic information

Entry
Database: PDB / ID: 3pjv
TitleStructure of Pseudomonas fluorescence LapD periplasmic domain
ComponentsCyclic dimeric GMP binding protein
KeywordsLYASE / binding protein / LapG
Function / homology
Function and homology information


cyclic-guanylate-specific phosphodiesterase activity / nucleotide binding / signal transduction / identical protein binding / membrane
Similarity search - Function
Translation Initiation Factor IF3 - #200 / LapD/MoxY periplasmic domain / Carboxypeptidase Inhibitor; Chain A / LapD/MoxY, periplasmic domain / LapD/MoxY periplasmic domain, C-terminal / LapD/MoxY periplasmic domain / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily ...Translation Initiation Factor IF3 - #200 / LapD/MoxY periplasmic domain / Carboxypeptidase Inhibitor; Chain A / LapD/MoxY, periplasmic domain / LapD/MoxY periplasmic domain, C-terminal / LapD/MoxY periplasmic domain / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Translation Initiation Factor IF3 / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / GGDEF domain profile. / GGDEF domain / Other non-globular / Nucleotide cyclase / Special / Reverse transcriptase/Diguanylate cyclase domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Diguanylate cyclase/phosphodiesterase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7727 Å
AuthorsSondermann, H. / Navarro, M.V.A.S. / Chatterjee, D.
CitationJournal: Plos Biol. / Year: 2011
Title: Structural Basis for c-di-GMP-Mediated Inside-Out Signaling Controlling Periplasmic Proteolysis.
Authors: Navarro, M.V. / Newell, P.D. / Krasteva, P.V. / Chatterjee, D. / Madden, D.R. / O'Toole, G.A. / Sondermann, H.
History
DepositionNov 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.pdbx_leaving_atom_flag / _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_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_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Cyclic dimeric GMP binding protein
F: Cyclic dimeric GMP binding protein


Theoretical massNumber of molelcules
Total (without water)28,5152
Polymers28,5152
Non-polymers00
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-43 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.488, 71.408, 110.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cyclic dimeric GMP binding protein


Mass: 14257.615 Da / Num. of mol.: 2 / Fragment: UNP Residues 22-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf0-1 / Gene: lapD, Pfl01_0131 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3KK31
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22% PEG monomethyl ether 2,000, 0.15 M Potassium bromide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9769 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 1, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9769 Å / Relative weight: 1
ReflectionResolution: 1.7727→30.08 Å / Num. obs: 32517 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.7727→1.83 Å / % possible all: 96.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6_289)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7727→30.08 Å / SU ML: 0.23 / σ(F): 0.34 / Phase error: 22.94 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.224 2000 6.31 %
Rwork0.2026 --
obs0.204 31705 97.18 %
all-32680 -
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.627 Å2 / ksol: 0.365 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.6109 Å2-0 Å20 Å2
2---9.5214 Å20 Å2
3---0.9105 Å2
Refinement stepCycle: LAST / Resolution: 1.7727→30.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 0 304 2249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062029
X-RAY DIFFRACTIONf_angle_d0.9742785
X-RAY DIFFRACTIONf_dihedral_angle_d13.225737
X-RAY DIFFRACTIONf_chiral_restr0.064333
X-RAY DIFFRACTIONf_plane_restr0.004358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7727-1.8170.32851260.28861869X-RAY DIFFRACTION87
1.817-1.86610.321340.27181985X-RAY DIFFRACTION93
1.8661-1.9210.27361360.24692027X-RAY DIFFRACTION94
1.921-1.9830.20621390.21152067X-RAY DIFFRACTION96
1.983-2.05390.25031440.20512133X-RAY DIFFRACTION99
2.0539-2.13610.2331420.2042111X-RAY DIFFRACTION99
2.1361-2.23330.22671450.20692152X-RAY DIFFRACTION99
2.2333-2.3510.21921430.19282129X-RAY DIFFRACTION99
2.351-2.49820.21891450.20452141X-RAY DIFFRACTION99
2.4982-2.6910.25541450.20352161X-RAY DIFFRACTION99
2.691-2.96160.24221480.2082198X-RAY DIFFRACTION99
2.9616-3.38970.22511460.20932184X-RAY DIFFRACTION100
3.3897-4.26870.20271510.17922232X-RAY DIFFRACTION100
4.2687-30.08440.20291560.19832316X-RAY DIFFRACTION98
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)
10.76520.5031-0.06061.73270.44830.93790.0932-0.25360.05420.1664-0.18230.14530.0772-0.20.08030.10380.00720.0150.10780.01640.108425.74543.75663.5379
21.01830.1358-0.20093.2328-0.29940.51170.07720.0634-0.2709-0.0951-0.1704-0.9266-00.03060.10540.0904-0.01350.02840.10120.02270.205537.412744.897261.1383
30.3288-0.0743-0.19940.39760.63511.0125-0.37410.0118-0.0848-0.03970.07340.3561-0.0512-0.12230.28490.28330.07430.04590.16630.00940.25128.091117.543966.6853
40.4998-0.0986-0.12740.3851-0.11240.0541-0.14540.1417-0.08990.33150.02850.01310.469-0.04790.16830.26420.04350.03160.2411-0.01280.133512.401235.759990.6582
51.4433-0.924-1.70421.26181.33621.559-0.14160.05120.41350.19020.2076-0.35130.3234-0.1525-0.05040.11650.03120.03070.14740.02850.148724.952826.767771.1629
61.0955-0.5744-1.0051.54420.07842.24910.19340.09680.3154-0.04740.012-0.2109-0.1011-0.0155-0.17070.12960.0022-0.00020.1207-0.02370.081619.134233.694776.9802
71.4275-0.5388-0.68110.3085-0.00531.8803-0.18730.2857-0.2848-0.02140.0216-0.03620.2999-0.5270.21670.1928-0.02230.05110.1986-0.00470.076311.233827.501377.6095
81.15391.20380.40111.53780.64810.30590.08380.0833-0.23050.21160.0617-0.32330.0326-0.0033-0.15980.1455-0.0135-0.03270.1311-0.02410.162920.406629.265950.5538
91.45560.55350.50590.20220.10421.59690.17040.1424-0.28470.15390.0364-0.7222-0.38370.1425-0.2490.2663-0.0416-0.05790.12930.00650.205733.57159.743164.1806
100.0977-0.22140.21641.17880.03141.16260.0926-0.0013-0.11380.0809-0.0191-0.27750.1876-0.1371-0.06340.0583-0.0209-0.00550.03730.01940.006422.268735.781758.7191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain D and resid 24:71)
2X-RAY DIFFRACTION2(chain D and resid 72:95)
3X-RAY DIFFRACTION3(chain D and resid 100:114)
4X-RAY DIFFRACTION4(chain D and resid 115:126)
5X-RAY DIFFRACTION5(chain D and resid 127:150)
6X-RAY DIFFRACTION6(chain F and resid 24:74)
7X-RAY DIFFRACTION7(chain F and resid 75:99)
8X-RAY DIFFRACTION8(chain F and resid 100:116)
9X-RAY DIFFRACTION9(chain F and resid 117:126)
10X-RAY DIFFRACTION10(chain F and resid 127:150)

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