PDB-3rht: Crystal structure of type 1 glutamine amidotransferase (GATase1)-...

ID or keywords:

Entry

Database: PDB / ID: 3rht

Title

Crystal structure of type 1 glutamine amidotransferase (GATase1)-like protein from Planctomyces limnophilus

Components

(GATase1)-like protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

metal ion binding
Similarity search - Function

Biological species

Planctomyces limnophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.83 Å

Authors

Michalska, K. / Li, H. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of type 1 glutamine amidotransferase (GATase1)-like protein from Planctomyces limnophilus
Authors: Michalska, K. / Li, H. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

History

Deposition	Apr 12, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 27, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3rht.cif.gz	420.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3rht.ent.gz	361.1 KB	Display	PDB format
PDBx/mmJSON format	3rht.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3rht_validation.pdf.gz	465.9 KB	Display	wwPDB validaton report
Full document	3rht_full_validation.pdf.gz	470.1 KB	Display
Data in XML	3rht_validation.xml.gz	42.5 KB	Display
Data in CIF	3rht_validation.cif.gz	62 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rh/3rht ftp://data.pdbj.org/pub/pdb/validation_reports/rh/3rht	HTTPS FTP

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Related structure data

Similar structure data	3ldf-d 4jxi-2 2klf-d 3obj-d 2etw-d 4m8d-6 3vse-3 5e7i-2 6cvf-1 3vse-1 Search similar-shape structures by Omokage search (details) 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: APC100657

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: (GATase1)-like protein

B: (GATase1)-like protein

C: (GATase1)-like protein

D: (GATase1)-like protein

hetero molecules

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

1

A: (GATase1)-like protein

D: (GATase1)-like protein

hetero molecules

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

2

B: (GATase1)-like protein

C: (GATase1)-like protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	42.287, 126.827, 101.964
Angle α, β, γ (deg.)	90.00, 96.60, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Protein , 1 types, 4 molecules ABCD

#1: Protein	(GATase1)-like protein Mass: 28587.254 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Planctomyces limnophilus (bacteria) / Strain: DSM 3776 / Gene: Plim_2614 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: D5SQH6

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Non-polymers , 6 types, 616 molecules

#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 595 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.22 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.16 M calcium acetate, 0.08 M sodium cacodylate, 14.4% PEG8000, 20% glycerol, pH 6.5, 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: 0.97929 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 5, 2011 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97929 Å / Relative weight: 1
Reflection	Resolution: 1.83→50 Å / Num. all: 93377 / Num. obs: 93329 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / B_iso Wilson estimate: 18.7 Å² / R_merge(I) obs: 0.093 / Net I/σ(I): 19.5
Reflection shell	Resolution: 1.83→1.86 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.607 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4567 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
SHELX		model building
MLPHARE		phasing
DM		model building
ARP/wARP		model building
Coot		model building
PHENIX		model building
REFMAC	5.5.0109	refinement
HKL-3000		data reduction
HKL-3000		data scaling
SHELX		phasing
DM		phasing
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.83→50 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.948 / SU B: 5.365 / SU ML: 0.075 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19172	1383	1.5 %	RANDOM
R_work	0.15754	-	-	-
all	0.15803	93207	-	-
obs	0.15803	93207	99.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 18.098 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.95 Å²	0 Å²	-0.35 Å²
2-	-	1.23 Å²	0 Å²
3-	-	-	-0.36 Å²

Refinement step

Cycle: LAST / Resolution: 1.83→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7752	0	73	595	8420

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.021	8103
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	5286
X-RAY DIFFRACTION	r_angle_refined_deg	1.44	1.943	11062
X-RAY DIFFRACTION	r_angle_other_deg	0.937	3	12892
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.8	5	1022
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.113	24.143	350
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.416	15	1232
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.001	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	1213
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	9138
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1620
X-RAY DIFFRACTION	r_mcbond_it	0.766	1.5	5058
X-RAY DIFFRACTION	r_mcbond_other	0.247	1.5	2074
X-RAY DIFFRACTION	r_mcangle_it	1.312	2	8095
X-RAY DIFFRACTION	r_scbond_it	2.416	3	3045
X-RAY DIFFRACTION	r_scangle_it	3.693	4.5	2967

LS refinement shell

Resolution: 1.832→1.88 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.295	103	-
R_work	0.263	6552	-
obs	-	6655	97.42 %

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	3.8417	-0.4331	1.7749	1.4911	0.4526	2.8424	0.0068	-0.5094	-0.1189	0.2688	0.0006	0.0801	-0.028	-0.2802	-0.0073	0.1001	-0.0149	-0.0017	0.2021	0.0345	0.0323	-4.0739	46.1029	34.3467
2	1.531	0.1064	0.0743	0.8294	-0.1446	2.3182	0.0196	-0.2049	-0.2923	0.0923	-0.0249	-0.0564	0.2476	0.0826	0.0053	0.1003	-0.0053	-0.0122	0.0997	0.0439	0.13	3.8951	35.3414	24.2757
3	3.2106	-0.8402	2.8981	3.6189	-5.4052	21.1292	0.0885	0.3529	-0.2472	0.0049	-0.1621	-0.1265	0.7221	0.6437	0.0737	0.0943	0.0016	-0.0155	0.1287	-0.11	0.1395	1.4302	35.493	-1.9492
4	1.778	-0.4169	0.1754	1.2852	0.0173	1.6577	0.0051	-0.214	-0.2689	0.1492	0.0263	0.1173	0.1598	-0.2662	-0.0314	0.0733	-0.0586	-0.0042	0.1268	0.0247	0.0834	-7.655	38.2023	23.601
5	4.5276	1.3352	-0.9012	2.2124	-1.0955	3.2472	0.0492	0.5563	0.5851	-0.0944	-0.0289	0.1563	-0.3561	-0.0615	-0.0203	0.1049	0.0117	-0.0302	0.1475	0.0961	0.0988	11.7164	47.365	55.7996
6	2.295	0.1634	-0.3978	1.2745	-0.2794	1.7578	0.0735	0.0392	0.3204	0.0072	-0.0912	-0.0606	-0.2179	0.1513	0.0177	0.0531	-0.0232	-0.026	0.039	0.0212	0.0863	20.884	45.9592	70.9458
7	10.3865	1.861	-1.0502	14.8041	0.5693	7.9468	0.4119	-1.1345	-0.6571	0.6977	-0.4668	-0.6327	0.2161	0.1383	0.0548	0.1128	-0.0578	-0.087	0.224	0.1179	0.0973	17.3873	21.1572	89.3378
8	2.4545	0.6196	0.1469	1.3509	0.0764	1.6991	0.0192	0.069	0.3379	-0.0113	-0.0426	0.1208	-0.2009	-0.0854	0.0234	0.0364	0.0151	0.0023	0.0123	0.0099	0.0501	10.3497	43.7501	70.2148
9	3.3429	1.6717	0.4715	2.3353	0.3734	1.7548	-0.2095	0.4137	-0.5446	-0.5188	0.134	-0.2754	0.2675	0.0137	0.0755	0.2326	-0.0015	0.0946	0.1296	-0.0837	0.1634	11.588	13.5746	53.8594
10	1.7434	0.4123	0.0281	2.0315	0.1327	1.3213	-0.0034	0.0168	-0.3583	-0.0541	-0.0999	-0.1111	0.1943	-0.0972	0.1033	0.0553	-0.0041	0.0293	0.0211	-0.0035	0.1017	6.7911	14.4858	70.8583
11	2.0812	1.7385	0.4502	14.7852	6.6269	3.6375	0.1631	-0.4229	-0.0427	0.4468	-0.4852	0.4837	0.2001	-0.2071	0.3221	0.0575	-0.036	-0.0016	0.1351	0.0158	0.0475	8.5313	26.3847	85.9353
12	2.2242	0.9989	-0.2343	1.8434	-0.0285	1.2863	-0.09	0.0778	-0.4934	-0.1395	-0.0299	-0.3761	0.1857	0.1348	0.1199	0.0548	0.0341	0.0382	0.0306	-0.001	0.1483	17.4602	15.8689	67.8951
13	3.8483	0.4488	-0.7257	6.5281	-1.6386	6.9804	0.1246	-0.1126	0.5417	0.0311	-0.0135	-0.0283	-0.3978	0.1332	-0.1111	0.0427	-0.0031	0.0024	0.0183	-0.0412	0.1257	-2.6861	67.465	12.8938
14	3.6004	-2.406	-0.008	2.9489	-0.0727	1.392	0.1441	0.0807	0.5235	-0.0539	-0.0511	-0.1776	-0.3362	0.0106	-0.093	0.1211	-0.0055	0.0197	0.0625	-0.0198	0.1453	-4.2407	69.7404	10.4932
15	1.6406	0.8535	-0.5034	2.7987	-1.0951	2.0355	0.0861	0.1631	0.2916	-0.0004	0.0099	0.2761	-0.2942	-0.27	-0.096	0.0751	0.0487	0.0042	0.142	-0.0026	0.0965	-15.9335	64.6356	3.7052
16	1.8513	-0.2903	-0.0507	1.3115	0.0135	1.5665	0.0311	0.2128	-0.0255	-0.1271	-0.02	-0.0224	0.0543	-0.0572	-0.0111	0.0351	-0.01	-0.004	0.0971	-0.0282	0.0148	-2.7586	50.8368	0.1235

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 58
2	X-RAY DIFFRACTION	2	A	59 - 164
3	X-RAY DIFFRACTION	3	A	165 - 187
4	X-RAY DIFFRACTION	4	A	188 - 254
5	X-RAY DIFFRACTION	5	B	3 - 49
6	X-RAY DIFFRACTION	6	B	50 - 169
7	X-RAY DIFFRACTION	7	B	170 - 183
8	X-RAY DIFFRACTION	8	B	184 - 254
9	X-RAY DIFFRACTION	9	C	3 - 69
10	X-RAY DIFFRACTION	10	C	70 - 157
11	X-RAY DIFFRACTION	11	C	158 - 186
12	X-RAY DIFFRACTION	12	C	187 - 254
13	X-RAY DIFFRACTION	13	D	3 - 13
14	X-RAY DIFFRACTION	14	D	14 - 63
15	X-RAY DIFFRACTION	15	D	64 - 116
16	X-RAY DIFFRACTION	16	D	117 - 254

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