PDB-7cjg: Structural and kinetic characterization of Porphyromonas gingival...

ID or keywords:

Entry

Database: PDB / ID: 7cjg

Title

Structural and kinetic characterization of Porphyromonas gingivalis glutaminyl cyclase

Components

Glutamine cyclotransferase-related protein

Keywords

ANTIBIOTIC /

glutaminyl cyclase /

pyroglutamate / prophyromonas gingivalis

Function / homology

Glutaminyl-peptide cyclotransferase-like / Peptidase M28 / Peptidase family M28 /

acyltransferase activity / Prokaryotic membrane lipoprotein lipid attachment site profile. /

5,6-DIMETHYLBENZIMIDAZOLE /

NITRATE ION / Glutamine cyclotransferase-related protein

Function and homology information

Biological species

Porphyromonas gingivalis (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Ruiz-Carrillo, D. / Lamers, S. / Feng, Q. / Yu, S. / Sun, B. / Jiang, J. / Lukman, M.

Funding support

China, 1items

Citation

Journal: Biol.Chem. / Year: 2021
Title: Structural and kinetic characterization of Porphyromonas gingivalis glutaminyl cyclase.
Authors: Lamers, S. / Feng, Q. / Cheng, Y. / Yu, S. / Sun, B. / Lukman, M. / Jiang, J. / Ruiz-Carrillo, D.

History

Deposition	Jul 10, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 5, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jun 9, 2021	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Nov 29, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7cjg.cif.gz	332.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7cjg.ent.gz	274.8 KB	Display	PDB format
PDBx/mmJSON format	7cjg.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cj/7cjg ftp://data.pdbj.org/pub/pdb/validation_reports/cj/7cjg	HTTPS FTP

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Related structure data

Related structure data	7cjeSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7cje-1 6qql-1 7cje-2 5fyr-1 3b3c-d 5qtx-d 6y88-4 6qql-2 6b77-d 5yby-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	#35 - Nov 2002 Ferritin and Transferrin similarity (2) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Glutamine cyclotransferase-related protein

B: Glutamine cyclotransferase-related protein

hetero molecules

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

1

A: Glutamine cyclotransferase-related protein

hetero molecules

defined by author&software
Evidence: gel filtration
37 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glutamine cyclotransferase-related protein

hetero molecules

defined by author&software
37 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	91.117, 91.117, 165.063
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID
1	1	1	(CHAIN 'A' AND (RESID 41 THROUGH 50 OR RESID 52...	A
2	1	1	(CHAIN 'B' AND (RESID 41 THROUGH 50 OR RESID 52...	B

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Protein , 1 types, 2 molecules AB

#1: Protein	Glutamine cyclotransferase-related protein Mass: 36565.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyromonas gingivalis (strain ATCC BAA-308 / W83) (bacteria) Strain: ATCC BAA-308 / W83 / Gene: PG_2157 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7MT37

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Non-polymers , 6 types, 344 molecules

#2: Chemical	ChemComp-DMD / 5,6-DIMETHYLBENZIMIDAZOLE / Dimethylbenzimidazole Mass: 146.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₀N₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-NO3 / NITRATE ION / Nitrate Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO₃
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 2.7 Å³/Da / Density % sol: 54.52 %
Crystal grow	Temperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Purified PgQC was concentrated up to 50 mg/ml and it was mixed in a 1:0.7 volume ratio with the crystallization buffer 0.1 M TRIS pH 8.0, 0.3 M MgNO3(H2O)6, 24% (w/v) PEG8000) incubating at 14 C

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Data collection

Diffraction	Mean temperature: 150 K / Serial crystal experiment: N
Diffraction source	Source: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.54184 Å
Detector	Type: Bruker PHOTON II / Detector: PIXEL / Date: Jun 22, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54184 Å / Relative weight: 1
Reflection	Resolution: 2→45.56 Å / Num. obs: 103509 / % possible obs: 99.9 % / Redundancy: 24 % / B_iso Wilson estimate: 31.75 Å² / R_merge(I) obs: 0.2057 / Net I/σ(I): 27.83
Reflection shell	Resolution: 2→2.07 Å / Redundancy: 15.1 % / R_merge(I) obs: 1.565 / Mean I/σ(I) obs: 1.76 / Num. unique obs: 5383 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.12_2829	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7CJE

7cje

Resolution: 2→32.06 Å / SU ML: 0.258 / Cross valid method: THROUGHOUT / σ(F): 1.358 / Phase error: 21.987
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.215	5166	4.991 %	RANDOM
R_work	0.179	-	-	-
obs	0.18	103501	99.9 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 48.83 Å²

Refinement step

Cycle: LAST / Resolution: 2→32.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4385	0	49	333	4767

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4541
X-RAY DIFFRACTION	f_angle_d	0.576	6167
X-RAY DIFFRACTION	f_dihedral_angle_d	12.873	2590
X-RAY DIFFRACTION	f_chiral_restr	0.043	642
X-RAY DIFFRACTION	f_plane_restr	0.003	810

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type
1	1	A	X-RAY DIFFRACTION	POSITIONAL
1	2	B	X-RAY DIFFRACTION	POSITIONAL

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2-2.0227	0.3487	174	0.335	3296	X-RAY DIFFRACTION	100
2.0227-2.0465	0.3389	172	0.3191	3248	X-RAY DIFFRACTION	100
2.0465-2.0715	0.3266	171	0.2933	3357	X-RAY DIFFRACTION	100
2.0715-2.0977	0.3325	171	0.2975	3232	X-RAY DIFFRACTION	100
2.0977-2.1253	0.3312	169	0.2808	3260	X-RAY DIFFRACTION	100
2.1253-2.1544	0.2918	173	0.2595	3274	X-RAY DIFFRACTION	100
2.1544-2.1852	0.2905	168	0.2409	3238	X-RAY DIFFRACTION	100
2.1852-2.2178	0.3014	176	0.2615	3393	X-RAY DIFFRACTION	100
2.2178-2.2524	0.435	169	0.3574	3209	X-RAY DIFFRACTION	100
2.2524-2.2893	0.3135	167	0.2953	3268	X-RAY DIFFRACTION	100
2.2893-2.3288	0.2866	181	0.2114	3301	X-RAY DIFFRACTION	100
2.3288-2.3711	0.2501	169	0.2081	3229	X-RAY DIFFRACTION	100
2.3711-2.4167	0.241	176	0.1921	3307	X-RAY DIFFRACTION	100
2.4167-2.4661	0.2206	175	0.1779	3281	X-RAY DIFFRACTION	100
2.4661-2.5197	0.2117	170	0.171	3302	X-RAY DIFFRACTION	100
2.5197-2.5782	0.2389	173	0.169	3246	X-RAY DIFFRACTION	100
2.5782-2.6427	0.1954	172	0.1664	3268	X-RAY DIFFRACTION	100
2.6427-2.7141	0.2049	174	0.1688	3281	X-RAY DIFFRACTION	100
2.7141-2.7939	0.1856	175	0.1641	3275	X-RAY DIFFRACTION	100
2.7939-2.884	0.2021	175	0.1647	3283	X-RAY DIFFRACTION	100
2.884-2.9871	0.1927	170	0.1685	3290	X-RAY DIFFRACTION	100
2.9871-3.1066	0.2373	175	0.1768	3274	X-RAY DIFFRACTION	100
3.1066-3.2478	0.1783	174	0.1763	3312	X-RAY DIFFRACTION	100
3.2478-3.4189	0.2433	174	0.1732	3240	X-RAY DIFFRACTION	100
3.4189-3.6328	0.2094	171	0.1589	3278	X-RAY DIFFRACTION	100
3.6328-3.9128	0.1694	178	0.1425	3274	X-RAY DIFFRACTION	100
3.9128-4.3058	0.162	169	0.1246	3306	X-RAY DIFFRACTION	100
4.3058-4.9269	0.1349	168	0.1133	3270	X-RAY DIFFRACTION	100
4.9269-6.2	0.1808	173	0.1478	3276	X-RAY DIFFRACTION	100
6.2-32.0632	0.2049	164	0.1799	3267	X-RAY DIFFRACTION	99

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	0.4766	-0.4258	0.3537	0.8475	0.4959	1.133	-0.1535	-0.1614	-0.0192	0.2149	0.1171	0.0319	-0.0898	-0.0147	-0.0048	0.2372	0.0352	0.01	0.1902	0.0008	0.2045	49.4907	-22.3916	13.2359
2	0.5382	-0.0834	-0.0775	0.4493	0.507	0.7782	-0.0375	0.0949	-0.2945	-0.0139	0.057	-0.0322	0.1044	-0.018	-0.0086	0.2495	0.0202	-0.0157	0.1948	0.005	0.3024	49.7082	-30.1446	7.3
3	0.0836	0.0459	0.0076	0.0973	0.1927	0.2252	-0.0398	0.2271	-0.1187	-0.1395	0.1057	0.0702	-0.1739	-0.0002	0.0003	0.3178	-0.0024	0.001	0.2413	-0.0018	0.2193	52.3459	-12.3129	3.9211
4	0.2079	0.0314	0.1119	0.1567	0.2276	0.3372	0.0492	0.1536	-0.2152	-0.1718	-0.1305	0.1369	0.1789	-0.2297	0	0.2543	0.0174	-0.0031	0.3316	-0.032	0.3195	39.3429	-26.3195	3.2698
5	0.5496	0.2664	0.1435	0.6897	1.2829	0.977	-0.0497	0.1848	-0.2573	-0.1721	0.0621	-0.0218	-0.1099	-0.0589	0.03	0.2649	0.0141	0.004	0.291	-0.0387	0.2371	50.4725	-27.5429	-8.6596
6	0.5377	0.1187	-0.3035	0.3316	0.4779	0.7787	0.0069	0.1104	-0.1378	-0.1469	0.0869	-0.1792	-0.0752	0.2633	0	0.2874	-0.0048	0.0068	0.2716	-0.0293	0.2944	58.8393	-25.1028	-0.1828
7	0.1777	-0.3744	0.0432	0.3832	0.175	1.0445	0.0868	0.1536	-0.0712	-0.0648	-0.103	-0.0219	0.3109	0.0063	-0.0133	0.3014	-0.0195	-0.0129	0.2616	-0.0584	0.2885	32.9407	-9.3127	16.9135
8	0.3456	-0.5902	-0.1414	1.0031	0.275	1.0943	0.0442	0.0438	-0.0271	0.1221	-0.0598	0.1598	0.319	-0.0701	-0.0072	0.2632	-0.048	0.0136	0.1926	0.0087	0.2543	31.3404	-5.3072	26.9435
9	0.2572	-0.0338	-0.0704	1.3834	-0.0667	0.3207	0.0623	0.3249	-0.0497	0.1225	-0.1752	0.4203	-0.2325	-0.42	-0.1009	0.2534	-0.034	0.0353	0.5384	-0.0003	0.3965	17.4377	0.2853	27.6413
10	0.5883	-0.1564	-0.1266	1.2801	0.3566	1.3408	0.0252	0.0873	0.1111	-0.0823	-0.0664	0.0953	-0.2075	-0.177	0	0.2288	0.035	0.0028	0.2125	0.0191	0.2539	32.1326	9.0527	22.9049

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 41 THROUGH 111 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 112 THROUGH 150 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 151 THROUGH 179 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 180 THROUGH 218 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 219 THROUGH 294 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 295 THROUGH 328 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 41 THROUGH 82 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 83 THROUGH 179 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 180 THROUGH 202 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 203 THROUGH 328 )

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