PDB-3fx3: Structure of a putative cAMP-binding regulatory protein from Sili...

ID or keywords:

Entry

Database: PDB / ID: 3fx3

Title

Structure of a putative cAMP-binding regulatory protein from Silicibacter pomeroyi DSS-3

Components

Cyclic nucleotide-binding protein

Keywords

cAMP-binding protein / helix_turn_helix / cAMP Regulatory protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function

Biological species

Ruegeria pomeroyi (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.2 Å

Authors

Cuff, M.E. / Zhou, M. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: Structure of a putative cAMP-binding regulatory protein from Silicibacter pomeroyi DSS-3
Authors: Cuff, M.E. / Zhou, M. / Freeman, L. / Joachimiak, A.

History

Deposition	Jan 19, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 24, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.3	Nov 20, 2024	Group: 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_site 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3fx3.cif.gz	111.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3fx3.ent.gz	84.8 KB	Display	PDB format
PDBx/mmJSON format	3fx3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3fx3_validation.pdf.gz	454.2 KB	Display	wwPDB validaton report
Full document	3fx3_full_validation.pdf.gz	456.7 KB	Display
Data in XML	3fx3_validation.xml.gz	24.9 KB	Display
Data in CIF	3fx3_validation.cif.gz	34 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fx/3fx3 ftp://data.pdbj.org/pub/pdb/validation_reports/fx/3fx3	HTTPS FTP

-
Related structure data

Similar structure data	3h3z-d 5ea1-d 4lp7-2 4by5-2 1zqs-d 8icg-d 8icu-d 4by5-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: apc88413

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#48 - Dec 2003 Catabolite Activator Protein similarity (8) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (5) #251 - Nov 2020 Adenylyl Cyclase similarity (5)

Deposited unit

A: Cyclic nucleotide-binding protein

B: Cyclic nucleotide-binding protein

hetero molecules

53.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	137.728, 137.728, 94.626
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3

Details

authors state that the biological assembly is unknown but likely a dimer

#1: Protein	Cyclic nucleotide-binding protein Mass: 26405.201 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruegeria pomeroyi (bacteria) / Strain: DSS-3 / Gene: SPOA0323 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5LKQ8
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 3.27 Å³/Da / Density % sol: 62.39 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.49M NaH2PO4, 0.91M K2HPO4, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.97926,0.97940

Detector

Type: CUSTOM-MADE / Detector: CCD / Date: Dec 1, 2007

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97926	1
2	0.9794	1

Reflection

Redundancy: 7 % / Av σ(I) over netI: 35.95 / Number: 236761 / R_merge(I) obs: 0.079 / Χ²: 2.35 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 33872 / % possible obs: 99.7

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.42	50	96	1	0.075	10.779	6.3
4.31	5.42	99.6	1	0.057	5.195	6.5
3.76	4.31	100	1	0.056	3.773	6.8
3.42	3.76	100	1	0.062	3.028	7
3.17	3.42	100	1	0.07	2.377	7
2.99	3.17	100	1	0.086	1.959	7.1
2.84	2.99	100	1	0.108	1.605	7.2
2.71	2.84	100	1	0.135	1.347	7.1
2.61	2.71	100	1	0.166	1.123	7.2
2.52	2.61	100	1	0.191	1.014	7.2
2.44	2.52	100	1	0.22	0.989	7.2
2.37	2.44	100	1	0.273	0.964	7.2
2.31	2.37	100	1	0.34	0.928	7.2
2.25	2.31	100	1	0.409	0.881	7.2
2.2	2.25	99.7	1	0.491	0.935	6.5

Reflection

Resolution: 2.2→50 Å / Num. all: 33872 / Num. obs: 33872 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7 % / B_iso Wilson estimate: 44.6 Å² / R_merge(I) obs: 0.079 / Χ²: 2.347 / Net I/σ(I): 35.955

Reflection shell

Resolution: 2.2→2.25 Å / Redundancy: 6.5 % / R_merge(I) obs: 0.491 / Num. unique all: 2284 / Χ²: 0.935 / % possible all: 99.7

-
Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2.2 Å / D res low: 50 Å / FOM : 0 / FOM acentric: 0.428 / FOM centric: 0 / Reflection: 0 / Reflection acentric: 33750 / Reflection centric: 0

Phasing MAD set

R cullis centric: 0 / Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Loc centric: 0 / Power centric: 0 / Reflection centric: _

ID	R cullis acentric	Loc acentric	Power acentric	Reflection acentric
1	1.85	0.3	0	33750
2	0.89	12	0.77	33604

Phasing MAD set shell

R cullis centric: 0 / Loc centric: 0 / Power centric: 0 / Reflection centric: _

ID	Resolution (Å)	R cullis acentric	Loc acentric	Power acentric	Reflection acentric
1	13.46-50	1.07	1	0	113
1	7.77-13.46	1.18	1.2	0	581
1	5.47-7.77	1.61	0.9	0	1438
1	4.21-5.47	1.19	0.7	0	2608
1	3.43-4.21	1.23	0.4	0	4119
1	2.89-3.43	2	0.3	0	5992
1	2.5-2.89	6.82	0.2	0	8171
1	2.2-2.5	9.46	0.1	0	10728
2	13.46-50	0.72	18.5	1.98	107
2	7.77-13.46	0.63	16	2.1	567
2	5.47-7.77	0.71	14.9	1.78	1430
2	4.21-5.47	0.79	15.3	1.31	2599
2	3.43-4.21	0.85	14.7	0.95	4106
2	2.89-3.43	0.9	11.5	0.81	5974
2	2.5-2.89	0.96	10.2	0.57	8143
2	2.2-2.5	0.99	11.2	0.31	10678

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	41.32611	0.867	0.888	0.038	0
2	Se	33.1231	0.966	0.865	-0.009	0
3	Se	50.45021	0.785	0.87	0.049	0
4	Se	34.117	0.65	0.782	0.073	0
5	Se	43.09872	0.596	0.679	0.274	0
6	Se	40.91866	0.456	0.51	0.351	0
7	Se	65.09601	0.593	0.842	-0.095	0
8	Se	72.02515	0.603	0.578	0.45	0
9	Se	67.81525	0.66	0.732	0.172	0
10	Se	138.67497	0.419	0.457	0.459	0
11	Se	89.13187	0.647	0.709	0.186	0
12	Se	39.83096	0.867	0.889	0.038	-0.116
13	Se	36.43557	0.967	0.866	-0.009	-0.093
14	Se	48.84646	0.785	0.87	0.049	-0.11
15	Se	34.62918	0.65	0.782	0.073	-0.087
16	Se	38.22009	0.596	0.679	0.273	-0.078
17	Se	42.17036	0.456	0.51	0.351	-0.078
18	Se	60.48792	0.593	0.841	-0.095	-0.047
19	Se	76.92637	0.603	0.579	0.45	-0.066
20	Se	63.68171	0.66	0.732	0.171	-0.042
21	Se	149.55197	0.419	0.457	0.459	-0.069
22	Se	99.54771	0.647	0.709	0.185	-0.029

Phasing MAD shell

Resolution (Å)	FOM acentric	Reflection acentric	Reflection
13.46-50	0.729	113
7.77-13.46	0.797	581	-1073768760
5.47-7.77	0.791	1438
4.21-5.47	0.723	2608
3.43-4.21	0.636	4119	135909581
2.89-3.43	0.554	5992	3
2.5-2.89	0.372	8171	-1
2.2-2.5	0.177	10728

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 33750

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
8.5-100	53.6	0.881	508
6.92-8.5	39.5	0.926	514
5.98-6.92	40.3	0.922	577
5.35-5.98	39.5	0.927	653
4.88-5.35	41.8	0.931	764
4.52-4.88	39.8	0.937	795
4.22-4.52	41	0.941	884
3.98-4.22	40.9	0.937	946
3.78-3.98	43.6	0.92	970
3.6-3.78	45.4	0.916	1023
3.45-3.6	45.2	0.914	1094
3.31-3.45	46.1	0.918	1134
3.19-3.31	44.1	0.913	1177
3.08-3.19	48.5	0.894	1213
2.98-3.08	48.5	0.896	1234
2.89-2.98	50.4	0.879	1299
2.81-2.89	51.6	0.88	1337
2.74-2.81	55.1	0.87	1374
2.67-2.74	55.5	0.861	1383
2.6-2.67	57.8	0.862	1443
2.54-2.6	60.1	0.873	1496
2.49-2.54	62.1	0.88	1492
2.44-2.49	62.3	0.868	1564
2.39-2.44	65.9	0.875	1536
2.34-2.39	68.4	0.865	1648
2.3-2.34	66.7	0.85	1625
2.25-2.3	72.6	0.831	1630
2.2-2.25	77.5	0.737	2437

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	5	phasing
REFMAC		refinement
PDB_EXTRACT	3.006	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building

Refinement

Method to determine structure:

MAD / Resolution: 2.2→31.54 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.95 / WR_factor R_free: 0.223 / WR_factor R_work: 0.181 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.893 / SU B: 9.288 / SU ML: 0.108 / SU R Cruickshank DPI: 0.199 / SU R_free: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.171
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.218	1713	5.1 %	RANDOM
R_work	0.181	-	-	-
all	0.183	33749	-	-
obs	0.183	33749	99.31 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 115.23 Å² / B_iso mean: 36.656 Å² / B_iso min: 21.21 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.26 Å²	-0.63 Å²	0 Å²
2-	-	-1.26 Å²	0 Å²
3-	-	-	1.89 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→31.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3464	0	42	304	3810

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	3658
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2462
X-RAY DIFFRACTION	r_angle_refined_deg	1.422	1.97	4978
X-RAY DIFFRACTION	r_angle_other_deg	0.882	3.001	5998
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.784	5	464
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.289	23.291	158
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.303	15	617
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.959	15	31
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	570
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	4070
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	732
X-RAY DIFFRACTION	r_mcbond_it	0.711	1.5	2296
X-RAY DIFFRACTION	r_mcbond_other	0.182	1.5	914
X-RAY DIFFRACTION	r_mcangle_it	1.396	2	3710
X-RAY DIFFRACTION	r_scbond_it	2.414	3	1362
X-RAY DIFFRACTION	r_scangle_it	3.862	4.5	1268

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.312	135	-
R_work	0.224	2387	-
all	-	2522	-
obs	-	-	98.82 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.5455	0.2754	-0.4352	2.3568	-0.5245	0.7341	-0.0459	0.2791	-0.1315	-0.2322	0.0583	0.3626	0.0783	-0.1949	-0.0124	0.0455	0.0012	-0.0456	0.0954	-0.0391	0.0854	42.968	52.4712	33.9267
2	1.5923	0.1258	-0.0347	1.8488	-0.647	0.984	0.0549	0.0264	0.1945	0.1397	0.039	0.1604	-0.174	-0.0808	-0.0939	0.091	0.0245	0.0333	0.0741	0.0243	0.0414	50.9555	79.7071	31.8625

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 225
2	X-RAY DIFFRACTION	2	B	2 - 232

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi