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- PDB-3pfm: Crystal structure of a EAL domain of GGDEF domain protein from Ps... -

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Basic information

Entry
Database: PDB / ID: 3pfm
TitleCrystal structure of a EAL domain of GGDEF domain protein from Pseudomonas fluorescens Pf
ComponentsGGDEF domain protein
KeywordsSIGNALING PROTEIN / PSI2 / MCSG / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics / EAL domain
Function / homology
Function and homology information


signal transduction / membrane
Similarity search - Function
LapD/MoxY, periplasmic domain / LapD/MoxY periplasmic domain, C-terminal / LapD/MoxY periplasmic domain / EAL domain / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain ...LapD/MoxY, periplasmic domain / LapD/MoxY periplasmic domain, C-terminal / LapD/MoxY periplasmic domain / EAL domain / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / GGDEF domain profile. / GGDEF domain / HAMP domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Cyclic dimeric GMP binding protein LapD
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.908 Å
AuthorsNocek, B. / Stein, A. / Marshall, N. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a EAL domain of GGDEF domain protein from Pseudomonas fluorescens Pf
Authors: Nocek, B. / Stein, A. / Marshall, N. / Clancy, S. / Joachimiak, A.
History
DepositionOct 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Oct 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GGDEF domain protein


Theoretical massNumber of molelcules
Total (without water)28,0921
Polymers28,0921
Non-polymers00
Water543
1
A: GGDEF domain protein

A: GGDEF domain protein


Theoretical massNumber of molelcules
Total (without water)56,1852
Polymers56,1852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y+1/2,z1
Buried area1180 Å2
ΔGint-12 kcal/mol
Surface area22030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.657, 107.861, 159.046
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein GGDEF domain protein


Mass: 28092.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf-5 / Gene: PFL_0131 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q4KKF5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 6 Å3/Da / Density % sol: 79.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 3.0 M NaCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2010 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. all: 15103 / Num. obs: 15097 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 37
Reflection shellResolution: 2.9→3 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1436 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
Auto-Rickshawphasing
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.908→40 Å / SU ML: 0.38 / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.237 703 4.99 %RANDOM
Rwork0.1875 ---
all0.195 14805 --
obs0.1898 14102 92.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.62 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-50.7549 Å2-0 Å2-0 Å2
2---15.0563 Å20 Å2
3----35.6985 Å2
Refinement stepCycle: LAST / Resolution: 2.908→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1868 0 0 3 1871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081908
X-RAY DIFFRACTIONf_angle_d1.1492593
X-RAY DIFFRACTIONf_dihedral_angle_d21.623674
X-RAY DIFFRACTIONf_chiral_restr0.072296
X-RAY DIFFRACTIONf_plane_restr0.004336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9082-3.13260.38261190.31352226X-RAY DIFFRACTION79
3.1326-3.44780.28391550.23982595X-RAY DIFFRACTION91
3.4478-3.94640.24621420.17382739X-RAY DIFFRACTION96
3.9464-4.9710.18121540.14422859X-RAY DIFFRACTION98
4.971-43.96690.22441330.18282980X-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)
14.66314.3101-2.74034.2225-2.57997.8552-2.56612.5192-0.69920.69430.3083-2.07891.08622.15111.43281.9306-0.42390.12171.3820.02170.660924.759611.029883.412
22.0067-0.55251.86079.6516-7.03755.3063-2.5289-1.9118-2.98731.19742.5255-0.1189-1.22460.2969-0.32951.49610.0245-0.15921.37840.21280.419323.69615.714178.4591
32.043-0.6737-0.39132.7727-0.10631.5884-0.1429-0.6363-0.061.13940.45010.46460.1249-1.1407-0.20011.0712-0.14590.06220.9516-0.0060.738221.62490.654366.2331
46.7871-1.37415.92256.5113-4.89979.8171-0.6676-0.75070.01980.39580.70070.4663-1.7203-0.64220.51130.4018-0.2532-0.06060.42410.06230.67720.599712.196541.3306
52.2764-0.57611.2363-0.3856-0.23461.3143-0.0868-0.54550.25230.2630.0390.18880.5681-1.08320.26360.78970.0155-0.01030.8538-0.09860.510718.42397.021953.0906
63.2816-2.7394-2.58114.01082.7462.29271.0199-1.31991.16480.8131-0.86481.48051.2651-4.1741-0.98561.026-0.0731-0.07781.85190.17961.109912.5687.896967.5412
71.51031.1949-0.14723.14440.85240.74660.7562-0.93070.33541.7307-0.8668-0.7137-1.5024-0.51340.11451.414-0.05110.00511.02770.12080.493628.78919.458671.0747
80.9344-0.02022.24590.89861.11696.6143-0.1530.0264-1.4036-0.1801-0.6127-0.0108-0.199-0.32510.18551.16140.05390.16620.8550.13550.764229.56460.573164.5949
95.3342.32835.77624.38084.48927.6493-0.1216-0.6924-0.1864-0.8213-1.10150.8272-0.6333-0.1760.78680.62690.03480.09180.7791-0.06020.891925.8486-4.62155.6379
103.38142.3249-0.42885.55232.26611.7855-0.0408-1.5370.526-1.0556-0.93981.0229-0.4154-1.22590.34641.09970.1080.19480.69450.02760.62925.3333-0.514650.0828
112.50950.1973-0.65130.2355-0.83746.82480.11120.0396-0.40240.48550.0729-0.50640.7955-0.28710.09380.81890.0506-0.15180.55610.10020.55536.5363-0.064756.2571
128.2247-0.61562.8475.1859-2.15251.73561.267-1.5086-2.26450.4503-1.4903-0.098-0.36050.27490.53240.9945-0.11270.34651.37280.22961.03145.267210.920455.8795
133.4021-3.27740.63377.55842.8593.16430.386-1.0341-0.64120.86350.8674-1.16181.21652.3598-0.44010.7170.10240.35081-0.02530.975243.98080.065750.4687
140.6401-1.84160.28464.84580.32893.07370.4449-0.56740.23172.6936-0.3957-1.8516-0.2858-0.7541-0.02340.90850.2631-0.01410.64780.06861.081936.077514.371450.5455
155.21023.3725-2.86589.23613.12675.0680.8587-0.43591.65121.8092-2.19982.52380.884-0.29150.89770.85120.21050.41691.1912-0.08060.874843.935116.845346.8151
162.9373.04671.10822.9691.04050.22970.4208-0.8885-0.4058-1.0258-0.20181.2077-0.3161-0.72030.0580.70750.16870.00460.7954-0.08680.751233.490915.763747.8625
175.31342.71660.80851.4854-0.45955.0863-1.15810.54431.37480.066-0.24250.1096-1.61880.190.65090.95750.1577-0.16810.6495-0.13330.937728.245328.296743.8568
186.1614-2.36480.33747.0949-0.14140.0113-0.96320.5036-1.2739-4.9506-2.2758-1.8851-0.1674-0.92092.39021.31660.20610.28570.63420.02281.246638.536215.269837.2591
195.5969-1.379-0.84454.05082.33071.3111-0.05-0.05520.6396-0.98210.13570.6247-0.9975-0.43970.08130.94990.1931-0.0980.7418-0.04480.905722.55121.194542.976
201.46880.9638-0.63763.0178-0.23390.21630.35350.17850.5205-1.7399-0.15580.07081.2045-0.77140.19640.77170.01190.01820.6024-0.0550.770617.770910.368949.176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 407:411)
2X-RAY DIFFRACTION2(chain A and resid 412:416)
3X-RAY DIFFRACTION3(chain A and resid 417:431)
4X-RAY DIFFRACTION4(chain A and resid 432:437)
5X-RAY DIFFRACTION5(chain A and resid 438:454)
6X-RAY DIFFRACTION6(chain A and resid 455:460)
7X-RAY DIFFRACTION7(chain A and resid 461:475)
8X-RAY DIFFRACTION8(chain A and resid 476:481)
9X-RAY DIFFRACTION9(chain A and resid 482:489)
10X-RAY DIFFRACTION10(chain A and resid 490:500)
11X-RAY DIFFRACTION11(chain A and resid 501:535)
12X-RAY DIFFRACTION12(chain A and resid 536:544)
13X-RAY DIFFRACTION13(chain A and resid 545:554)
14X-RAY DIFFRACTION14(chain A and resid 555:567)
15X-RAY DIFFRACTION15(chain A and resid 568:573)
16X-RAY DIFFRACTION16(chain A and resid 574:586)
17X-RAY DIFFRACTION17(chain A and resid 587:607)
18X-RAY DIFFRACTION18(chain A and resid 608:612)
19X-RAY DIFFRACTION19(chain A and resid 613:633)
20X-RAY DIFFRACTION20(chain A and resid 634:648)

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