PDB-3cit: Crystal structure of the GAF domain of a putative sensor histidin...

ID or keywords:

Entry

Database: PDB / ID: 3cit

Title

Crystal structure of the GAF domain of a putative sensor histidine kinase from Pseudomonas syringae pv. tomato

Components

Sensor histidine kinase

Keywords

TRANSFERASE / MEGA: 3.30.450.40 / structural genomics / sensor histidine kinase / Pseudomonas syringae / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

phosphorelay sensor kinase activity / protein dimerization activity / membrane
Similarity search - Function

Biological species

Pseudomonas syringae pv. tomato (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.9 Å

Authors

Cuff, M.E. / Li, H. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of the GAF domain of a putative sensor histidine kinase from Pseudomonas syringae pv. tomato
Authors: Cuff, M.E. / Li, H. / Abdullah, J. / Joachimiak, A.

History

Deposition	Mar 11, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 13, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software
Revision 1.3	Mar 26, 2025	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_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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	3cit_validation.pdf.gz	474.5 KB	Display	wwPDB validaton report
Full document	3cit_full_validation.pdf.gz	478.7 KB	Display
Data in XML	3cit_validation.xml.gz	20.6 KB	Display
Data in CIF	3cit_validation.cif.gz	28.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ci/3cit ftp://data.pdbj.org/pub/pdb/validation_reports/ci/3cit	HTTPS FTP

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Related structure data

Similar structure data	6tt4-1 6qs1-1 3nxq-2 7e0c-d 5amb-2 3uba-d 6en6-3 3nxq-1 Search similar-shape structures by Omokage search (details) 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: APC87806.2

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#183 - Mar 2015 Phototropin similarity (1) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (1) #9 - Sep 2000 Lysozyme similarity (1)

Deposited unit

A: Sensor histidine kinase

B: Sensor histidine kinase

hetero molecules

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

1

A: Sensor histidine kinase

B: Sensor histidine kinase

hetero molecules

A: Sensor histidine kinase

B: Sensor histidine kinase

hetero molecules

defined by software
72.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	107.471, 107.471, 67.698
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	A-321- HOH

Details

AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE IS UNKNOWN

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Protein , 1 types, 2 molecules AB

#1: Protein	Sensor histidine kinase Mass: 17452.578 Da / Num. of mol.: 2 / Fragment: Domain: Residues 18-174 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria) Species: Pseudomonas syringae group genomosp. 3 / Strain: DC3000 / Gene: PSPTO_2131 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q884G2

#1: Protein

Sensor histidine kinase

Mass: 17452.578 Da / Num. of mol.: 2 / Fragment: Domain: Residues 18-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas syringae pv. tomato (bacteria)
Species: Pseudomonas syringae group genomosp. 3 / Strain: DC3000 / Gene: PSPTO_2131 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q884G2

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Non-polymers , 5 types, 337 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-BME / BETA-MERCAPTOETHANOL Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.23 Å³/Da / Density % sol: 61.96 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M Bis-Tris propane pH 7.0, 1.5M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.9793, 0.9795

Detector

Type: CUSTOM-MADE / Detector: CCD / Date: Oct 7, 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	0.9793	1
2	0.9795	1

Reflection

Redundancy: 11 % / Av σ(I) over netI: 10.9 / Number: 393091 / R_merge(I) obs: 0.062 / Χ²: 1.36 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 35808 / % possible obs: 99.3

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.68	50	96.4	1	0.04	2.83	10.7
3.72	4.68	99.1	1	0.039	2.042	9.9
3.25	3.72	99.7	1	0.047	1.923	11
2.95	3.25	99.9	1	0.059	1.666	11.2
2.74	2.95	99.8	1	0.07	1.394	11.4
2.58	2.74	99.4	1	0.082	1.241	11.3
2.45	2.58	99.5	1	0.095	1.206	11.3
2.34	2.45	99.5	1	0.111	1.165	11.1
2.25	2.34	99.3	1	0.127	1.114	11.1
2.17	2.25	99.5	1	0.148	1.065	11
2.11	2.17	99.3	1	0.175	1.002	11
2.05	2.11	99.6	1	0.21	0.971	11
1.99	2.05	99.2	1	0.26	0.975	11
1.94	1.99	99.5	1	0.348	0.93	10.9
1.9	1.94	99.4	1	0.507	0.915	10.9

Reflection

Resolution: 1.9→50 Å / Num. all: 35808 / Num. obs: 35808 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 11 % / B_iso Wilson estimate: 27.6 Å² / R_merge(I) obs: 0.062 / Χ²: 1.361 / Net I/σ(I): 10.9

Reflection shell

Resolution: 1.9→1.94 Å / Redundancy: 10.9 % / R_merge(I) obs: 0.507 / Mean I/σ(I) obs: 4 / Num. unique all: 2357 / Χ²: 0.915 / % possible all: 99.4

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 1.9 Å / D res low: 50 Å / FOM : 0.24 / FOM acentric: 0.26 / FOM centric: 0 / Reflection: 35279 / Reflection acentric: 32644 / Reflection centric: 2635

Phasing MAD set

R cullis acentric: 1.71 / R cullis centric: 1 / Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Loc acentric: 0.1 / Loc centric: 0 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 32644 / Reflection centric: 2635

Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)	R cullis acentric	Loc acentric	Loc centric	Reflection acentric	Reflection centric
12.01-50	1.6	0.2	0.1	85	46
6.82-12.01	1.16	0.2	0.1	520	127
4.76-6.82	1.51	0.1	0.1	1331	211
3.66-4.76	1.09	0.1	0.1	2468	284
2.97-3.66	1.31	0.1	0.1	3980	371
2.5-2.97	2.13	0.1	0	5762	450
2.16-2.5	2.36	0	0	7985	536
1.9-2.16	2.85	0	0	10513	610

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z
1	Se	28.94595	-0.119	-0.5	-0.029
2	Se	23.00053	-0.273	-0.659	-0.274
3	Se	42.22318	0.002	-0.559	0.172
4	Se	76.72991	0.102	-0.579	-0.036

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	Reflection	Reflection acentric	Reflection centric
12.01-50	0.333	0.513	131	85	46
6.82-12.01	0.452	0.562	647	520	127
4.76-6.82	0.442	0.512	1542	1331	211
3.66-4.76	0.385	0.429	2752	2468	284
2.97-3.66	0.381	0.416	4351	3980	371
2.5-2.97	0.301	0.324	6212	5762	450
2.16-2.5	0.196	0.209	8521	7985	536
1.9-2.16	0.108	0.115	11123	10513	610

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 35279

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.82-100	60.9	0.794	514
6.23-7.82	58	0.882	513
5.33-6.23	59.3	0.886	630
4.73-5.33	60.1	0.908	707
4.3-4.73	63.4	0.921	768
3.97-4.3	63.8	0.906	838
3.7-3.97	59.1	0.908	922
3.48-3.7	59.6	0.899	979
3.3-3.48	57.8	0.899	1034
3.14-3.3	60.3	0.885	1062
3.01-3.14	60.1	0.892	1145
2.89-3.01	62.1	0.862	1155
2.78-2.89	61.6	0.877	1240
2.68-2.78	64.5	0.874	1240
2.6-2.68	61	0.873	1298
2.52-2.6	64.9	0.874	1320
2.45-2.52	63.8	0.865	1353
2.38-2.45	64.2	0.854	1434
2.32-2.38	64.8	0.868	1443
2.26-2.32	65.2	0.86	1479
2.21-2.26	65.6	0.864	1514
2.16-2.21	68.5	0.857	1559
2.11-2.16	71.4	0.851	1568
2.07-2.11	73.6	0.855	1656
2.03-2.07	75.3	0.854	1666
1.99-2.03	75.9	0.846	1684
1.96-1.99	75.5	0.816	1695
1.9-1.96	80.7	0.721	2863

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	5	phasing
REFMAC		refinement
PDB_EXTRACT	3.004	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: 1.9→31.22 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.949 / SU B: 4.275 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.112
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2	1760	5 %	RANDOM
R_work	0.165	-	-	-
all	0.167	35273	-	-
obs	0.167	35273	98.51 %	-

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 mean: 21.534 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.75 Å²	0.38 Å²	0 Å²
2-	-	0.75 Å²	0 Å²
3-	-	-	-1.13 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→31.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2310	0	68	324	2702

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.021	2493
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1715
X-RAY DIFFRACTION	r_angle_refined_deg	1.424	2.007	3379
X-RAY DIFFRACTION	r_angle_other_deg	0.964	3	4173
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.262	5	319
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.471	23.271	107
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.816	15	420
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.861	15	27
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	391
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2743
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	472
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	498
X-RAY DIFFRACTION	r_nbd_other	0.206	0.2	1855
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	1146
X-RAY DIFFRACTION	r_nbtor_other	0.086	0.2	1395
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.141	0.2	251
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.203	0.2	13
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.221	0.2	52
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.3	0.2	30
X-RAY DIFFRACTION	r_mcbond_it	1.24	1.5	1922
X-RAY DIFFRACTION	r_mcbond_other	0.253	1.5	632
X-RAY DIFFRACTION	r_mcangle_it	1.541	2	2499
X-RAY DIFFRACTION	r_scbond_it	2.491	3	990
X-RAY DIFFRACTION	r_scangle_it	3.638	4.5	877

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.233	107	-
R_work	0.202	2438	-
all	-	2545	-
obs	-	-	97.62 %

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	4.4867	-0.1947	3.1429	7.1937	-7.1242	10.3284	0.0218	-0.3201	0.6606	0.4524	0.0259	0.2139	-0.5667	-0.1233	-0.0478	0.0437	-0.0398	0.0478	-0.0167	-0.0482	0.057	80.7482	57.4605	0.5239
2	3.0786	0.6711	-0.2813	0.9138	-0.1055	0.8545	0.1708	-0.1765	-0.1833	0.1973	-0.1002	-0.0577	0.0463	-0.0149	-0.0706	0.0304	-0.0573	-0.0124	-0.0043	0.0081	-0.0408	72.8351	39.9002	1.6781
3	11.2961	-5.5091	1.4523	12.0029	4.9642	3.6406	-0.5966	-1.5805	-1.3999	1.4551	1.3923	0.4111	0.8315	0.1346	-0.7957	0.2804	0.137	-0.1107	0.2196	0.2639	0.1718	90.7979	28.1469	13.0755
4	48.5991	-2.3717	12.2098	72.9782	14.9408	6.3805	0.0146	2.8869	2.9981	-2.306	-0.8441	0.451	-1.0658	0.4359	0.8296	0.2133	0.0242	-0.0009	0.1994	0.1105	0.1963	87.0147	69.8427	-8.22
5	2.1305	0.468	0.2316	1.1915	0.3261	1.4997	0.1253	-0.0176	-0.25	0.0818	-0.0184	-0.1272	0.2108	0.0812	-0.1069	0.063	0	-0.0621	-0.0299	-0.0021	0.0094	100.2633	46.9121	-3.696
6	1.9671	0.8324	0.1861	2.0039	0.2461	0.2405	0.2019	-0.2036	-0.1702	0.1277	-0.0726	-0.098	0.0642	0.0579	-0.1294	0.0587	-0.029	-0.0647	0.0207	0.0136	-0.0118	101.3462	49.1828	2.9877

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	16 - 39	2 - 25
2	X-RAY DIFFRACTION	2	A	A	40 - 159	26 - 145
3	X-RAY DIFFRACTION	3	A	A	160 - 172	146 - 158
4	X-RAY DIFFRACTION	4	B	B	16 - 20	2 - 6
5	X-RAY DIFFRACTION	5	B	B	21 - 99	7 - 85
6	X-RAY DIFFRACTION	6	B	B	100 - 169	86 - 155

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 337 molecules

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