PDB-2g9i: Crystal structure of homolog of F420-0:gamma-Glutamyl Ligase from...

ID or keywords:

Entry

Database: PDB / ID: 2g9i

Title

Crystal structure of homolog of F420-0:gamma-Glutamyl Ligase from Archaeoglobus fulgidus Reveals a Novel Fold.

Components

F420-0:gamma-glutamyl ligase

Keywords

LIGASE / CofE homolog / homolog of F420-0:gamma-Glutamyl Ligase / gamma-Glutamyl Ligase / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

coenzyme F420-0:L-glutamate ligase / coenzyme F420-1:gamma-L-glutamate ligase / coenzyme F420-0:L-glutamate ligase activity / coenzyme F420-1:gamma-L-glutamate ligase activity / F420-0 metabolic process / GTP binding / metal ion binding
Similarity search - Function

Biological species

Archaeoglobus fulgidus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.5 Å

Authors

Nocek, B. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: J.Mol.Biol. / Year: 2007
Title: Structure of an amide bond forming F(420):gamma-glutamyl ligase from Archaeoglobus fulgidus -- a member of a new family of non-ribosomal peptide synthases.
Authors: Nocek, B. / Evdokimova, E. / Proudfoot, M. / Kudritska, M. / Grochowski, L.L. / White, R.H. / Savchenko, A. / Yakunin, A.F. / Edwards, A. / Joachimiak, A.

History

Deposition	Mar 6, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 4, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name

Remark 300

BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	2g9i_validation.pdf.gz	441.9 KB	Display	wwPDB validaton report
Full document	2g9i_full_validation.pdf.gz	452.2 KB	Display
Data in XML	2g9i_validation.xml.gz	20.1 KB	Display
Data in CIF	2g9i_validation.cif.gz	27.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g9/2g9i ftp://data.pdbj.org/pub/pdb/validation_reports/g9/2g9i	HTTPS FTP

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Related structure data

Related structure data	2phnC C: citing same article (ref.)
Similar structure data	2c77-d 6240 3q1p-d 4quq-d 5ly3-d 6sar-d 6fiu-d 4ikm-d 2pmd-2 5l50-d 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: APC5730

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: F420-0:gamma-glutamyl ligase

B: F420-0:gamma-glutamyl ligase

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	100.386, 100.386, 92.960
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ARG / End label comp-ID: CYS / Refine code: 3 / Auth seq-ID: 2 - 248 / Label seq-ID: 2 - 248

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

Details

Crystallographic analysis of the asymmetric unit content indicates that dimer is a biological relavant oligomeric form, which is consistent with reported biochemical data (Li et al., Biochemistry; 2003; 42(32) pp 9771 - 9778)

#1: Protein	F420-0:gamma-glutamyl ligase Mass: 27483.018 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: cofE / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O28028, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

F420-0:gamma-glutamyl ligase

Mass: 27483.018 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: cofE / Plasmid: pET15b / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O28028, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.13 Å³/Da / Density % sol: 42.24 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 30% PEG 2K MME, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2005
Radiation	Monochromator: Double Crystal / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.5→40 Å / Num. all: 16992 / Num. obs: 16992 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 30.4 % / R_merge(I) obs: 0.109 / Net I/σ(I): 40.3
Reflection shell	Resolution: 2.5→2.54 Å / Redundancy: 24.1 % / Mean I/σ(I) obs: 5.1 / R_sym value: 0.565 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
SBC-Collect		data collection
HKL-2000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
MLPHARE		phasing
DM		phasing
SOLVE		phasing
RESOLVE		phasing
Coot		model building
CCP4		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.5→40 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.93 / SU B: 19.162 / SU ML: 0.216 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / σ(I): 0 / ESU R: 0.814 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25484	855	5 %	RANDOM
R_work	0.19021	-	-	-
all	0.1935	16936	-	-
obs	0.19351	16081	99.67 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 26.536 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.26 Å²	0 Å²	0 Å²
2-	-	1.26 Å²	0 Å²
3-	-	-	-2.52 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3548	0	0	98	3646

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	3637
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.826	1.995	4905
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.279	5	471
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.608	23.019	159
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.431	15	666
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.039	15	44
X-RAY DIFFRACTION	r_chiral_restr	0.12	0.2	572
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2718
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.238	0.2	1665
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.319	0.2	2513
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.175	0.2	159
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.924	1.5	2404
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.61	2	3753
X-RAY DIFFRACTION	r_scbond_it	2.742	3	1348
X-RAY DIFFRACTION	r_scangle_it	4.271	4.5	1152
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Number	Type	Rms dev position (Å)	Weight position
884	tight positional	0.07	0.05
782	loose positional	0.48	5
884	tight thermal	0.18	0.5
782	loose thermal	1.63	10

LS refinement shell

Resolution: 2.5→2.565 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.289	67	-
R_work	0.22	1142	-
obs	-	-	99.18 %

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	9.8866	6.8565	3.2932	8.3355	3.4196	3.796	0.102	-0.408	0.1235	-0.2697	-0.3124	0.5444	-0.4573	-0.711	0.2105	0.1244	0.1623	-0.0139	0.2927	0.0818	0.0277	9.5823	21.8386	17.6408
2	3.8774	1.3047	0.2712	2.9099	-1.0629	2.933	0.0356	-0.091	0.2675	-0.328	-0.159	0.4713	-0.5513	-0.6221	0.1233	0.2436	0.2069	-0.0429	0.3738	0.0048	0.0813	9.4159	26.4972	12.2731
3	3.0347	-2.3253	0.8987	5.4778	-1.5382	2.7339	0.2002	0.0816	-0.5049	0.0135	-0.0962	0.2948	0.4971	-0.3438	-0.104	0.1682	-0.0693	-0.05	0.1863	0.0182	0.1645	20.8498	-2.8577	18.8612
4	2.2119	2.5021	-2.0696	6.2959	-2.2174	18.4845	0.0537	0.386	-0.3529	-0.0055	-0.0204	0.125	0.4804	-0.5125	-0.0334	0.2153	-0.0352	-0.1018	0.1687	-0.0109	0.1698	25.1266	-4.4822	18.8392
5	5.2558	2.2926	-0.9677	1.5057	-2.3371	7.4299	0.1828	0.1266	-0.6618	0.3896	-0.2117	-0.9968	0.4477	0.5309	0.0289	0.2392	0.0588	-0.1429	0.0667	0.0127	0.399	34.9253	-0.1409	23.5582
6	2.3777	3.1183	1.6706	8.4727	-0.3486	2.6449	0.0142	0.0975	-0.0216	-0.0895	0.227	-0.2491	-0.0122	-0.3894	-0.2412	0.1173	0.0252	-0.0409	0.1445	0.0194	0.1027	27.6791	4.9874	17.2641
7	17.3113	-6.8855	-3.1287	16.0669	12.4158	9.9289	-0.2661	-1.3338	0.1697	0.1357	0.7262	1.4935	0.2414	-0.6037	-0.4601	0.3989	0.0673	0.1925	0.4094	0.1751	0.2571	12.292	1.1767	24.9852
8	1.7121	-1.367	0.6483	5.4158	-2.3028	3.2245	0.1031	0.24	-0.261	-0.5214	-0.1186	0.0898	0.0785	-0.3408	0.0155	0.1281	0.0735	-0.0191	0.2653	-0.0009	0.0727	17.8509	10.8728	9.5877
9	1.1433	-0.6213	2.009	2.999	-0.4419	3.689	0.0093	-0.0307	0.0853	-0.3801	-0.0823	0.2081	-0.3922	-0.4934	0.0731	0.265	0.2017	-0.0065	0.3562	0.0356	0.0523	13.4862	23.4113	6.8114
10	9.9157	-4.2327	1.2533	2.2526	0.8334	4.3587	-0.1149	0.2823	-0.0488	-0.1146	0.302	-0.1951	0.145	-0.0131	-0.1872	0.1603	0.0049	0.0159	0.0971	0.0394	0.0485	29.8225	13.2486	25.2695
11	1.1891	-0.3531	0.5333	1.5763	-0.7595	3.4271	0.1151	0.2456	0.019	-0.0182	-0.1915	-0.2475	-0.491	0.0438	0.0763	0.1767	0.0727	0.0308	0.169	0.0381	0.0476	29.6612	20.3708	17.9089
12	9.0531	-0.0219	-4.183	0.0261	-0.3777	7.6966	0.1942	-0.1009	0.0274	-0.2415	-0.0519	-0.0246	-0.7942	-0.057	-0.1423	0.2398	0.0786	0.065	0.1258	0.0218	0.0287	27.0855	24.6099	19.3346
13	3.7292	0.8087	0.6229	3.3285	-0.2046	5.8179	0.2238	-0.0767	0.0778	-0.1082	-0.2775	0.1575	-0.6177	-0.4281	0.0537	0.2162	0.1771	-0.0259	0.2218	0.0343	0.0217	17.4987	26.7081	16.5472
14	12.5847	-7.2811	3.7374	6.4489	-2.0846	2.6404	0.4268	0.9462	-0.1392	-0.4706	-0.3107	-0.3314	-0.2325	0.4563	-0.1161	0.1259	0.0089	0.0774	0.226	-0.0418	0.1098	38.5674	11.907	11.765
15	20.5175	-25.6566	-4.1978	39.4754	16.0455	16.6264	-0.6621	-0.4509	-0.7147	-0.2772	0.8215	-1.8344	-0.0365	-0.323	-0.1594	0.1696	0.1257	0.1164	0.1177	-0.0007	0.4221	44.4512	0.9058	20.0822
16	30.03	23.6303	-1.2848	24.1185	-2.7323	4.8977	-0.0783	0.922	1.8013	0.7601	0.4261	1.3246	-1.1163	-0.453	-0.3478	0.4907	0.1726	0.0203	0.1169	0.0976	0.091	21.0963	38.2462	25.2424
17	7.2661	3.1913	1.5955	2.3666	1.0008	2.498	-0.0957	-0.4914	0.9256	-0.4195	0.112	-0.2299	-1.1873	0.0408	-0.0163	0.7655	-0.0401	0.1677	0.0639	-0.0457	0.2661	33.0006	45.7146	32.948
18	11.1851	-0.4946	-1.8826	1.6497	1.2509	4.2701	0.4376	0.0424	0.624	-0.3834	-0.1517	-0.1462	-0.9698	-0.0805	-0.2859	0.4699	0.0097	0.099	0.068	0.005	0.0758	32.3278	36.6697	32.3886
19	12.6267	-3.0752	2.2729	3.6239	-0.024	0.5067	-0.3575	0.2818	0.758	0.4017	0.6605	-0.9474	-0.7363	0.8066	-0.303	0.3762	-0.2379	0.156	0.3536	-0.2071	0.3336	51.5522	36.9769	32.9868
20	9.6155	2.2912	0.7062	7.1023	0.6258	6.1468	0.2332	-0.0252	-0.1289	0.0455	-0.0944	-0.5551	-0.5893	0.9819	-0.1388	0.1355	-0.2209	0.0736	0.6653	-0.1514	0.1997	60.6301	24.1407	24.1943
21	13.0027	3.4987	-1.1537	4.9835	-1.4139	6.8128	0.4924	-0.7192	-0.284	0.5634	-0.2879	-0.4784	-0.3136	0.7499	-0.2045	0.1127	-0.0926	0.0009	0.3917	-0.1062	0.1557	53.1673	19.7035	29.6693
22	5.5206	0.0462	-3.7898	5.1341	2.9467	11.1985	0.231	-0.2159	-0.2531	0.1859	0.1113	-0.064	-0.363	0.6096	-0.3423	0.0562	-0.0397	0.0259	0.2873	-0.1259	0.2175	47.1527	19.1246	27.3195
23	4.8731	-1.5225	-0.6484	0.4757	0.2026	0.0863	0.4956	1.0826	0.8764	0.1315	-0.1192	0.0291	-0.2961	0.3847	-0.3764	0.4505	-0.2424	0.2585	0.3685	-0.0483	0.2999	48.2919	31.9713	23.9976
24	6.109	-1.8201	-3.5164	1.1054	2.2906	4.9777	0.2202	-0.116	0.3501	-0.1384	0.145	-0.3238	-0.8421	0.232	-0.3652	0.375	-0.0734	0.1254	0.1736	-0.067	0.1384	39.4468	35.0513	37.3078
25	2.3495	0.1209	0.5457	1.3573	0.4952	2.3638	0.1645	-0.2573	0.2616	-0.0834	-0.1542	-0.0579	-0.8321	-0.3007	-0.0103	0.4244	0.0595	0.0638	0.1717	-0.0208	0.0865	27.1206	37.4846	38.979
26	0.4032	-0.7978	-0.0824	3.3823	3.4382	5.9637	0.1107	0.1745	0.066	-0.0763	0.1132	-0.1269	-0.3678	0.2322	-0.224	0.1706	0.0322	0.0568	0.1648	0.0102	0.0741	36.3957	20.7868	20.6057
27	0.1057	0.456	-0.5955	9.0829	-1.9141	3.4174	-0.1659	-0.0803	-0.0456	-0.0225	0.2266	0.6272	0.0001	-0.4538	-0.0607	0.2095	0.0635	0.061	0.1862	0.0308	0.0438	25.2818	21.0666	36.2733
28	1.2265	0.3711	0.467	5.0377	-0.7894	5.2126	0.1336	0.0128	0.0883	-0.006	-0.0788	-0.0208	-0.5712	-0.2276	-0.0548	0.183	0.0746	0.0573	0.1377	0.024	0.0414	27.3014	25.8305	26.2098
29	3.121	-1.7111	0.1259	2.4656	1.3316	2.3297	-0.0973	-0.3197	-0.2463	0.2413	0.2471	0.0174	-0.1401	0.017	-0.1498	0.1429	-0.0058	0.0343	0.119	0.0521	0.036	33.2316	20.5	33.2647
30	72.7692	12.1635	-7.1264	15.7333	-2.166	23.4672	-0.0109	-1.4553	-1.0555	-0.2582	-0.5653	-0.3805	0.9275	0.7924	0.5762	0.0259	0.155	-0.1318	0.3873	-0.1388	0.2802	50.6402	5.5248	27.0933

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	1 - 20	1 - 20
2	X-RAY DIFFRACTION	2	A	A	21 - 37	21 - 37
3	X-RAY DIFFRACTION	3	A	A	38 - 70	38 - 70
4	X-RAY DIFFRACTION	4	A	A	71 - 84	71 - 84
5	X-RAY DIFFRACTION	5	A	A	85 - 93	85 - 93
6	X-RAY DIFFRACTION	6	A	A	94 - 109	94 - 109
7	X-RAY DIFFRACTION	7	A	A	110 - 116	110 - 116
8	X-RAY DIFFRACTION	8	A	A	117 - 133	117 - 133
9	X-RAY DIFFRACTION	9	A	A	134 - 150	134 - 150
10	X-RAY DIFFRACTION	10	A	A	151 - 155	151 - 155
11	X-RAY DIFFRACTION	11	A	A	156 - 176	156 - 176
12	X-RAY DIFFRACTION	12	A	A	189 - 205	189 - 205
13	X-RAY DIFFRACTION	13	A	A	206 - 226	206 - 226
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24	X-RAY DIFFRACTION	24	B	B	115 - 137	115 - 137
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29	X-RAY DIFFRACTION	29	B	B	212 - 245	212 - 245
30	X-RAY DIFFRACTION	30	B	B	246 - 249	246 - 249

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