PDB-2qm6: Crystal Structure of Helicobacter Pylori Gamma-Glutamyltranspepti...

ID or keywords:

Entry

Database: PDB / ID: 2qm6

Title

Crystal Structure of Helicobacter Pylori Gamma-Glutamyltranspeptidase in Complex with Glutamate

Components

(Gamma-glutamyltranspeptidase) x 2

Keywords

TRANSFERASE / NTN-HYDROLASE / GLUTAMYLTRANSPEPTIDASE

Function / homology

Function and homology information

gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process / negative regulation of cell cycle G1/S phase transition / glutathione biosynthetic process / negative regulation of T cell proliferation / positive regulation of interleukin-8 production
Similarity search - Function

Biological species

Helicobacter pylori (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Barycki, J.J. / Sand, A. / Boanca, G.

Citation

Journal: Biochemistry / Year: 2007
Title: Characterization of Helicobacter pylori gamma-glutamyltranspeptidase reveals the molecular basis for substrate specificity and a critical role for the tyrosine 433-containing loop in catalysis.
Authors: Morrow, A.L. / Williams, K. / Sand, A. / Boanca, G. / Barycki, J.J.

History

Deposition	Jul 14, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 12, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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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PDBx/mmCIF format	2qm6.cif.gz	225.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2qm6.ent.gz	180.1 KB	Display	PDB format
PDBx/mmJSON format	2qm6.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2qm6_validation.pdf.gz	468.3 KB	Display	wwPDB validaton report
Full document	2qm6_full_validation.pdf.gz	470.4 KB	Display
Data in XML	2qm6_validation.xml.gz	43.6 KB	Display
Data in CIF	2qm6_validation.cif.gz	65.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qm/2qm6 ftp://data.pdbj.org/pub/pdb/validation_reports/qm/2qm6	HTTPS FTP

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Related structure data

Related structure data	2qmcC 2nqoS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3fnm-d 2qmc-d 2nqo-d 5bpk-d 6sxv-d 6sxu-d 3uki-d 4kpb-d 1xvp-d 4bjr-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#166 - Oct 2013 Proteasome similarity (1) #235 - Jul 2019 AMPA Receptor similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #176 - Aug 2014 Dynein similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: Gamma-glutamyltranspeptidase

B: Gamma-glutamyltranspeptidase

C: Gamma-glutamyltranspeptidase

D: Gamma-glutamyltranspeptidase

hetero molecules

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

1

Idetical with deposited unit
defined by author

2

A: Gamma-glutamyltranspeptidase

B: Gamma-glutamyltranspeptidase

hetero molecules

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

3

C: Gamma-glutamyltranspeptidase

D: Gamma-glutamyltranspeptidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	54.983, 104.762, 91.910
Angle α, β, γ (deg.)	90.00, 91.85, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Gamma-glutamyltranspeptidase / Ggt Mass: 40577.379 Da / Num. of mol.: 2 / Fragment: residues 25-379 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP_1118 / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 / References: UniProt: O25743, gamma-glutamyltransferase
#2: Protein	Gamma-glutamyltranspeptidase / Ggt Mass: 20410.186 Da / Num. of mol.: 2 / Fragment: residues 380-567 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP_1118 / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 / References: UniProt: O25743, gamma-glutamyltransferase
#3: Chemical	ChemComp-GLU / GLUTAMIC ACID Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₉NO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 737 / 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: 2.17 Å³/Da / Density % sol: 43.29 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 200 MM HEPES, 25% PEG MME2000, 5 MG/ML PROTEIN, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2007
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. obs: 136302 / % possible obs: 99.4 % / Redundancy: 6.5 % / R_merge(I) obs: 0.075 / R_sym value: 0.088 / Net I/σ(I): 21.9
Reflection shell	Resolution: 1.6→1.66 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.384 / Mean I/σ(I) obs: 2.7 / R_sym value: 0.474 / % possible all: 99.3

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 2NQO

2nqo

Resolution: 1.6→32.93 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.963 / SU B: 2.697 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19017	13494	9.9 %	RANDOM
R_work	0.16652	-	-	-
obs	0.16888	122321	99.27 %	-

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: 15.361 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.07 Å²	0 Å²	-0.03 Å²
2-	-	0.42 Å²	0 Å²
3-	-	-	-0.35 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.085 Å	0.088 Å
Luzzati sigma a	0.05 Å	-

Refinement step

Cycle: LAST / Resolution: 1.6→32.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8050	0	20	737	8807

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	8305
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.228	1.97	11237
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.113	5	1078
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.347	25.359	334
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.737	15	1459
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.006	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	1255
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	6232
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	4026
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.303	0.2	5785
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.104	0.2	660
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	0.148	0.2	47
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.119	0.2	28
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	0.633	1.5	5472
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.939	2	8550
X-RAY DIFFRACTION	r_scbond_it	1.737	3	3197
X-RAY DIFFRACTION	r_scangle_it	2.741	4.5	2687
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.6→1.641 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.238	1010	-
R_work	0.187	8992	-
obs	-	-	99.05 %

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	1.5171	-0.1575	0.2841	0.4878	-0.0382	0.4273	0.0145	0.1112	-0.1871	-0.0872	-0.0078	0.0493	0.0987	-0.0747	-0.0067	-0.0016	-0.0075	-0.0003	0.0352	-0.0162	0.0321	35.87	-16.261	29.137
2	0.8234	-0.4139	-0.1148	0.6815	0.2351	0.8833	-0.0191	-0.0576	-0.0195	0.0059	0.0458	-0.0496	0.0344	0.0845	-0.0267	0.0183	0.0042	0.0016	0.0445	0.0057	0.0394	51.769	-13.468	38.792
3	0.3318	-0.1376	-0.0262	0.499	-0.055	0.5462	-0.0403	-0.047	-0.042	0.0545	0.0508	0.0557	-0.0391	-0.0257	-0.0105	0.0114	-0.0017	0.0008	0.0488	0.0002	0.0153	39.379	-2.002	40.532
4	0.4893	0.7109	-0.1298	3.5412	1.6886	1.4393	0.0522	0.096	0.2262	-0.0834	0.009	0.271	-0.3769	-0.412	-0.0611	0.062	-0.0004	-0.0121	0.0874	0.0143	0.0351	40.01	24.329	37.665
5	0.3706	-0.2244	-0.148	0.5883	0.1702	0.6429	-0.0113	-0.0359	-0.0056	0.0384	0.0368	-0.0319	-0.0277	0.0444	-0.0254	0.0113	-0.0026	0.0055	0.0382	0.003	0.0173	45	-5.257	40.572
6	0.5911	0.1062	-0.0218	1.0858	-0.0936	0.7874	-0.0439	0.0566	-0.0312	-0.0791	0.0621	0.0373	-0.0788	-0.0342	-0.0182	0.0409	-0.0046	-0.0027	0.064	-0.0016	0.0041	37.978	6.629	24.617
7	24.6435	14.5281	1.9001	9.563	2.391	1.7644	-0.3556	0.5694	-0.8474	-0.528	0.4023	-0.5238	-0.0591	0.0713	-0.0467	0.0512	-0.0107	-0.0218	0.0737	-0.0036	0.0663	36.433	-5.933	19.867
8	0.7617	0.3095	-0.196	1.0377	-0.226	1.0082	-0.0499	-0.0087	-0.1259	-0.1327	-0.0039	-0.0322	0.1174	0.0776	0.0539	0.0345	0.0224	0.0218	0.0297	0.007	0.0361	40.737	-8.599	-14.924
9	1.334	0.4077	-0.7643	1.7657	-0.7268	1.8133	-0.0785	0.0377	-0.0789	-0.1345	0.0975	0.1643	0.225	-0.1353	-0.019	0.0265	-0.0319	-0.0173	-0.0038	-0.006	0.0394	25.953	-15.886	-13.07
10	0.3316	0.148	-0.0464	0.7369	-0.0173	0.6793	-0.0165	0.0025	-0.0031	-0.1143	0.04	-0.0949	-0.0673	0.1166	-0.0236	0.0177	-0.0103	0.0145	0.0449	0.003	0.0091	46.618	10.652	-13.84
11	1.1709	0.2973	-0.2509	0.217	-0.6401	2.4015	-0.0194	0.0541	0.1913	-0.0452	0.0394	-0.0417	-0.1906	0.0326	-0.0201	0.0629	-0.0256	0.0142	-0.0014	0.0037	0.0276	44.618	27.167	-12.958
12	0.5864	0.2313	-0.19	0.765	-0.2595	0.8613	-0.0066	-0.0039	-0.0158	-0.1051	0.0078	0.0269	0.0001	-0.017	-0.0013	0.0282	0.013	0.0009	0.0192	-0.0006	0.0102	36.744	-0.149	-16.026
13	0.6409	-0.1941	-0.2038	1.2045	0.1874	0.7751	-0.013	-0.1031	-0.0473	0.102	0.0234	-0.0596	-0.0179	0.1141	-0.0103	0.0173	-0.0033	-0.0072	0.0761	0.0143	0.007	44.36	8.226	1.63
14	36.3794	-29.8022	-3.1767	25.1644	0.5441	5.9243	-1.1543	-1.0423	-0.2055	0.8851	0.885	0.4688	0.3031	0.2396	0.2693	0.102	0.0257	-0.0191	0.0799	0.0108	0.0802	42.756	-3.414	4.557

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	32 - 95	30 - 93
2	X-RAY DIFFRACTION	2	A	A	96 - 206	94 - 204
3	X-RAY DIFFRACTION	3	A	A	207 - 355	205 - 353
4	X-RAY DIFFRACTION	4	A	A	356 - 372	354 - 370
5	X-RAY DIFFRACTION	5	B	B	380 - 458	1 - 79
6	X-RAY DIFFRACTION	6	B	B	459 - 555	80 - 176
7	X-RAY DIFFRACTION	7	B	B	556 - 565	177 - 186
8	X-RAY DIFFRACTION	8	C	C	32 - 162	30 - 160
9	X-RAY DIFFRACTION	9	C	C	163 - 245	161 - 243
10	X-RAY DIFFRACTION	10	C	C	246 - 352	244 - 350
11	X-RAY DIFFRACTION	11	C	C	353 - 379	351 - 377
12	X-RAY DIFFRACTION	12	D	D	380 - 458	1 - 79
13	X-RAY DIFFRACTION	13	D	D	459 - 557	80 - 178
14	X-RAY DIFFRACTION	14	D	D	558 - 565	179 - 186

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