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- PDB-3icl: X-Ray Structure of Protein (EAL/GGDEF domain protein) from M.caps... -

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Basic information

Entry
Database: PDB / ID: 3icl
TitleX-Ray Structure of Protein (EAL/GGDEF domain protein) from M.capsulatus, Northeast Structural Genomics Consortium Target McR174C
ComponentsEAL/GGDEF domain protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics / Consortium / NESG / McR174C / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase ...Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
EAL/GGDEF domain protein
Similarity search - Component
Biological speciesMethylococcus capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SINGLE WAVELENGTH / Resolution: 2 Å
AuthorsKuzin, A. / Chen, Y. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Wang, H. / Everett, J.K. / Nair, R. ...Kuzin, A. / Chen, Y. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target McR174C
Authors: Kuzin, A. / Chen, Y. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJul 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 13, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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 / _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: EAL/GGDEF domain protein
B: EAL/GGDEF domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,65010
Polymers37,8822
Non-polymers7698
Water1,63991
1
A: EAL/GGDEF domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2294
Polymers18,9411
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EAL/GGDEF domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4216
Polymers18,9411
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.672, 75.950, 95.196
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 EAL/GGDEF domain protein


Mass: 18940.979 Da / Num. of mol.: 2 / Fragment: sequence database residues 61-223 / Mutation: E80K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus (bacteria) / Gene: MCA0337 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q60BX6
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 1.94 Å3/Da / Density % sol: 36.62 %
Crystal growTemperature: 293 K / pH: 3.5
Details: 0.1M Citric Acid, 2M Ammonium Sulfate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 9, 2009
RadiationProtocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 20466 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 23.68 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 26.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 4.68 / % possible all: 95.4

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Processing

Software
NameVersionClassificationNB
PHENIX1.4_115refinement
PDB_EXTRACT3data extraction
DENZOdata reduction
SCALEPACKdata scaling
Auto-Rickshawphasing
REFMACrefinement
RefinementMethod to determine structure: SINGLE WAVELENGTH / Resolution: 2→29.68 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 19.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.222 1046 5.11 %
Rwork0.208 --
obs0.216 20464 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.28 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 16.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.1427 Å20 Å20 Å2
2--0.0787 Å2-0 Å2
3---0.0641 Å2
Refinement stepCycle: LAST / Resolution: 2→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2446 0 40 91 2577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012517
X-RAY DIFFRACTIONf_angle_d1.3143415
X-RAY DIFFRACTIONf_dihedral_angle_d17.228920
X-RAY DIFFRACTIONf_chiral_restr0.093391
X-RAY DIFFRACTIONf_plane_restr0.006448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10610.27441540.23492663X-RAY DIFFRACTION98
2.1061-2.2380.23911470.2092733X-RAY DIFFRACTION100
2.238-2.41080.24011420.21082739X-RAY DIFFRACTION100
2.4108-2.65320.22251460.21882770X-RAY DIFFRACTION100
2.6532-3.03680.22111770.22432736X-RAY DIFFRACTION100
3.0368-3.82480.20591410.20612819X-RAY DIFFRACTION100
3.8248-29.68820.18661390.19082958X-RAY DIFFRACTION100
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)
10.44320.20450.24490.74430.15210.7129-0.02550.0864-0.0575-0.05730.09660.0383-0.08440.04530.38080.0849-0.0134-0.00180.05470.01250.044-11.41826.01069.7558
20.37290.07330.26460.61870.17120.80050.0380.00760.04120.04-0.0111-0.06250.01060.045-0.00010.02010.00280.00590.05240.00760.0522-7.683918.454135.8929
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA0 - 216
2X-RAY DIFFRACTION2chain BB7 - 217

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