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- PDB-4yme: Crystal structure of a sensory box/GGDEF family protein (CC_0091)... -

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Basic information

Entry
Database: PDB / ID: 4yme
TitleCrystal structure of a sensory box/GGDEF family protein (CC_0091) from Caulobacter crescentus CB15 at 1.40 A resolution (PSI Community Target, Shapiro)
Componentssensory box/GGDEF family protein
KeywordsLYASE / GGDEF domain / PF00990 family / ferredoxin-like fold / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


membrane => GO:0016020 / plasma membrane
Similarity search - Function
MHYT domain / Bacterial signalling protein N terminal repeat / MHYT domain profile. / PAS domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain ...MHYT domain / Bacterial signalling protein N terminal repeat / MHYT domain profile. / PAS 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 / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain / PAS domain / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized signaling protein CC_0091
Similarity search - Component
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Shapiro, L.
CitationJournal: To be published
Title: Crystal structure of a sensory box/GGDEF family protein (CC_0091) from Caulobacter crescentus CB15 at 1.40 A resolution (PSI Community Target, Shapiro)
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sensory box/GGDEF family protein


Theoretical massNumber of molelcules
Total (without water)16,7741
Polymers16,7741
Non-polymers00
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.429, 49.416, 82.905
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein sensory box/GGDEF family protein


Mass: 16774.033 Da / Num. of mol.: 1 / Fragment: UNP residues 372-528
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: ATCC 19089 / CB15 / Gene: CC_0091 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q9ABX9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (372-528) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (372-528) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.11 Å3/Da / Density % sol: 41.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M magnesium formate, 20% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97952 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 6, 2014
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 1.4→23.679 Å / Num. obs: 30788 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 6.17 % / Biso Wilson estimate: 19.725 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.03 / Rrim(I) all: 0.038 / Net I/σ(I): 15.62 / Num. measured all: 145154
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
1.4-1.450.5630.9461.414061584956501.187196.6
1.45-1.510.7940.5682.314933604960070.71699.3
1.51-1.580.9210.3383.714614588358580.42599.6
1.58-1.660.9590.2235.314096563556120.2899.6
1.66-1.760.9780.1557.414190566056250.19499.4
1.76-1.90.9930.08711.615090602859710.1199.1
1.9-2.090.9970.04818.814503581957290.0698.5
2.09-2.390.9980.0327.914742586357850.03998.7
2.39-3.010.9990.02235.414676585857430.02898
3.010.9990.01843.514249593155810.02394.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XDSNovember 3, 2014 BUILT=20141118data scaling
REFMAC5.8.0103refinement
XSCALEdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→23.679 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.23 / SU B: 2.939 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.064
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. A MET- ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 5. THE SAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2048 1546 5 %RANDOM
Rwork0.1827 29187 --
obs0.1839 30733 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.79 Å2 / Biso mean: 26.8077 Å2 / Biso min: 13.57 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å20 Å2-0 Å2
2---1.55 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.4→23.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1142 0 0 186 1328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221256
X-RAY DIFFRACTIONr_bond_other_d0.0020.021215
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.9691720
X-RAY DIFFRACTIONr_angle_other_deg1.01532806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8835186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80324.83962
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98215217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7521511
X-RAY DIFFRACTIONr_chiral_restr0.1130.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021509
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02282
X-RAY DIFFRACTIONr_mcbond_it1.6732.091655
X-RAY DIFFRACTIONr_mcbond_other1.6652.086654
X-RAY DIFFRACTIONr_mcangle_it2.7353.13825
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 117 -
Rwork0.356 2045 -
all-2162 -
obs--95.83 %
Refinement TLS params.Method: refined / Origin x: 21.9336 Å / Origin y: 17.3673 Å / Origin z: 9.2369 Å
111213212223313233
T0.0114 Å2-0.0028 Å20.0108 Å2-0.0073 Å2-0.0016 Å2--0.0138 Å2
L0.2404 °2-0.2939 °20.0214 °2-0.7286 °20.157 °2--0.4256 °2
S-0.0191 Å °0.0128 Å °-0.0133 Å °-0.0159 Å °-0.0102 Å °-0.0034 Å °-0.0078 Å °0.0223 Å °0.0293 Å °

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