6TTS | pdb_00006tts

Crystal structure of the GGDEF domain of DgcB from Caulobacter crescentus in complex with c-di-GMP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IGN	3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme
experimental model	PDB	3HVA	3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme
experimental model	PDB	3QYY	3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme
experimental model	PDB	3I5C	3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme
experimental model	PDB	4WXW	3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme
experimental model	PDB	3TVK	3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme
experimental model	PDB	4URG	3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme
experimental model	PDB	4ZVF	3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme
experimental model	PDB	4H54	3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme
experimental model	PDB	4ZMM	3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme
experimental model	PDB	3ICL	3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme
experimental model	PDB	4IOB	3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme
experimental model	PDB	5EUH	3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme
experimental model	PDB	3EZU	3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme
experimental model	PDB	4YME	3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	0.2 M LiSO4, 0.1 M NaAcet pH 5.5, 8% w/v PEG 20k, 8% v/v PEG 500 MME, 500 uM c-di-GMP, 1 mM GTP

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.5	α = 90
b = 64.5	β = 90
c = 246.76	γ = 90

Symmetry
Space Group	P 41 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2018-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.97947	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.5	64.5	99.9	0.159	0.183	0.088	0.813	8.3	7.2		19045			29.29

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.6	99		0.515	0.672	0.427	0.693	2.3	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme	2.5	50.76	1.34	18974	1002	99.8	0.2065	0.2035	0.2	0.2608	0.26	29.68

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	26.9272
f_angle_d	1.3588
f_chiral_restr	0.0664
f_bond_d	0.0098
f_plane_restr	0.0063

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2645
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms	260

Software

Software
Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.