PDB-4b6g: The Crystal Structure of the Neisserial Esterase D.

ID or keywords:

Entry

Database: PDB / ID: 4b6g

Title

The Crystal Structure of the Neisserial Esterase D.

Components

PUTATIVE ESTERASE

Keywords

HYDROLASE / FORMALDEHYDE DETOXIFICATION / ALPHA/BETA SERINE HYDROLASE

Function / homology

Function and homology information

S-formylglutathione hydrolase / S-formylglutathione hydrolase activity / formaldehyde catabolic process / carboxylic ester hydrolase activity / cytosol
Similarity search - Function

Biological species

NEISSERIA MENINGITIDIS MC58 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.4 Å

Authors

Counago, R.M. / Kobe, B.

Citation

Journal: Antioxid. Redox Signal. / Year: 2013
Title: A glutathione-dependent detoxification system is required for formaldehyde resistance and optimal survival of Neisseria meningitidis in biofilms.
Authors: Chen, N.H. / Counago, R.M. / Djoko, K.Y. / Jennings, M.P. / Apicella, M.A. / Kobe, B. / McEwan, A.G.

History

Deposition	Aug 13, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 14, 2012	Provider: repository / Type: Initial release
Revision 1.1	Feb 13, 2013	Group: Database references
Revision 1.2	Mar 28, 2018	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4b6g.cif.gz	331.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4b6g.ent.gz	277.3 KB	Display	PDB format
PDBx/mmJSON format	4b6g.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4b6g_validation.pdf.gz	407.3 KB	Display	wwPDB validaton report
Full document	4b6g_full_validation.pdf.gz	407.4 KB	Display
Data in XML	4b6g_validation.xml.gz	27.7 KB	Display
Data in CIF	4b6g_validation.cif.gz	43.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b6/4b6g ftp://data.pdbj.org/pub/pdb/validation_reports/b6/4b6g	HTTPS FTP

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Related structure data

Related structure data	3fcxS S: Starting model for refinement
Similar structure data	2q3y-d 4xu0-1 5l7g-d 5g3j-d 4de3-1 4xtw-1 1l9y-1 3sh9-2 2wk0-2 2ao6-d 4xtz-1 3v4a-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

Deposited unit

A: PUTATIVE ESTERASE

B: PUTATIVE ESTERASE

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

1

A: PUTATIVE ESTERASE

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

2

B: PUTATIVE ESTERASE

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

Unit cell

Length a, b, c (Å)	111.268, 111.268, 169.861
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein	PUTATIVE ESTERASE / S-FORMYLGLUTATHIONE HYDROLASE PROTEIN Mass: 32388.193 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NEISSERIA MENINGITIDIS MC58 (bacteria) / Strain: C311 / Variant: NUMBER 3 / Plasmid: PMSGC7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9JZ43, S-formylglutathione hydrolase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 726 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

PUTATIVE ESTERASE / S-FORMYLGLUTATHIONE HYDROLASE PROTEIN

Mass: 32388.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

NEISSERIA MENINGITIDIS MC58 (bacteria) / Strain: C311 / Variant: NUMBER 3 / Plasmid: PMSGC7 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9JZ43, S-formylglutathione hydrolase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 726 / 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: 2.23 Å³/Da / Density % sol: 45 % / Description: NONE
Crystal grow	pH: 6.5 Details: 25 MM BIS-TRIS (PH 6.5), 200 MM LITHIUM SULFATE AND 25% PEG 3350.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2010 / Details: SILICON MIRRORS (ADAPTIVE AND U-BENT)
Radiation	Monochromator: DOUBLE CRYSTAL MONOCHROMATOR (SI111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95369 Å / Relative weight: 1
Reflection	Resolution: 1.3→19.84 Å / Num. obs: 151514 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / B_iso Wilson estimate: 10.91 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 15.3
Reflection shell	Resolution: 1.3→1.37 Å / Redundancy: 5.1 % / R_merge(I) obs: 0.68 / Mean I/σ(I) obs: 2.3 / % possible all: 98

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FCX

3fcx

Resolution: 1.4→19.842 Å / SU ML: 0.09 / σ(F): 0 / Phase error: 13.36 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1539	3610	3 %
R_work	0.1431	-	-
obs	0.1434	121215	99.65 %

Solvent computation

Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 0 Å² / k_sol: 0 e/Å³

Displacement parameters

B_iso mean: 21.023 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→19.842 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4512	0	0	726	5238

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	4651
X-RAY DIFFRACTION	f_angle_d	1.222	6315
X-RAY DIFFRACTION	f_dihedral_angle_d	14.519	1690
X-RAY DIFFRACTION	f_chiral_restr	0.077	641
X-RAY DIFFRACTION	f_plane_restr	0.007	839

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 (%)
1.4-1.4184	0.2448	161	0.2209	4433	X-RAY DIFFRACTION	100
1.4184-1.4379	0.2222	111	0.219	4469	X-RAY DIFFRACTION	100
1.4379-1.4584	0.2566	134	0.2018	4471	X-RAY DIFFRACTION	100
1.4584-1.4801	0.1958	133	0.1915	4469	X-RAY DIFFRACTION	100
1.4801-1.5033	0.1897	126	0.184	4516	X-RAY DIFFRACTION	100
1.5033-1.5279	0.1762	132	0.1783	4444	X-RAY DIFFRACTION	100
1.5279-1.5542	0.1627	147	0.1645	4474	X-RAY DIFFRACTION	100
1.5542-1.5825	0.1772	122	0.1589	4493	X-RAY DIFFRACTION	100
1.5825-1.6129	0.1563	132	0.1544	4505	X-RAY DIFFRACTION	100
1.6129-1.6458	0.1512	135	0.1442	4477	X-RAY DIFFRACTION	100
1.6458-1.6816	0.158	127	0.1482	4499	X-RAY DIFFRACTION	100
1.6816-1.7207	0.1712	139	0.1489	4500	X-RAY DIFFRACTION	100
1.7207-1.7637	0.1665	153	0.1462	4492	X-RAY DIFFRACTION	100
1.7637-1.8114	0.1553	145	0.1379	4490	X-RAY DIFFRACTION	100
1.8114-1.8646	0.1372	143	0.1324	4511	X-RAY DIFFRACTION	100
1.8646-1.9248	0.1433	138	0.132	4523	X-RAY DIFFRACTION	100
1.9248-1.9935	0.1278	131	0.1295	4537	X-RAY DIFFRACTION	100
1.9935-2.0732	0.1503	121	0.131	4563	X-RAY DIFFRACTION	100
2.0732-2.1675	0.1348	140	0.1281	4532	X-RAY DIFFRACTION	100
2.1675-2.2816	0.1347	146	0.1288	4542	X-RAY DIFFRACTION	100
2.2816-2.4243	0.13	156	0.123	4553	X-RAY DIFFRACTION	100
2.4243-2.6111	0.1478	134	0.1329	4575	X-RAY DIFFRACTION	100
2.6111-2.8732	0.1518	142	0.1383	4593	X-RAY DIFFRACTION	100
2.8732-3.2873	0.1549	143	0.1428	4603	X-RAY DIFFRACTION	99
3.2873-4.1355	0.1479	180	0.1337	4592	X-RAY DIFFRACTION	98
4.1355-19.8436	0.1552	139	0.1429	4749	X-RAY DIFFRACTION	96

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	0.0347	0.0627	-0.0218	0.1193	-0.0446	0.0182	0.0187	-0.1132	0.0164	0.0339	-0.0025	0.0283	-0.0328	0.0467	0	0.1826	-0.0092	0.0013	0.1404	-0.0038	0.1437	21.01	102.0605	30.4042
2	0.088	0.0705	-0.0655	0.0649	-0.025	0.1368	-0.0017	0.0049	0.0635	0.0427	-0.0324	0.0395	-0.0623	0.0261	-0	0.1563	-0.0006	-0.0031	0.1252	-0.0035	0.1543	15.4846	99.6806	21.772
3	0.2427	0.0107	0.0643	0.4232	-0.0662	0.729	-0.0272	-0.0215	-0.0122	0.029	-0.0096	0.0119	-0.0387	0.0144	-0.0001	0.1286	-0.0013	0.0021	0.1141	0.0067	0.1257	18.6055	90.43	21.0711
4	0.2993	0.0182	0.0351	0.2539	0.0412	0.5666	-0.0221	0.0174	-0.0078	-0.0355	0.0013	0.0401	-0.0492	-0.026	0	0.1362	0.0017	0.0015	0.1268	0.0066	0.1338	14.9932	91.7852	9.7404
5	0.1786	-0.088	-0.0543	0.3604	0.1719	0.5099	0.0078	0.0682	-0.0744	-0.0645	-0.0354	0.0532	0.0532	-0.0969	-0	0.1499	-0.0047	-0.0043	0.1645	-0.0011	0.1645	9.4016	79.8831	5.6104
6	0.2236	-0.1251	0.0021	0.1147	0.1123	0.2849	0.0063	0.0274	-0.0402	0.0028	-0.032	0.0105	0.094	0.0622	-0	0.1649	0.0061	0.0077	0.1379	0.0002	0.1418	22.9752	75.7497	11.1054
7	0.4677	-0.0448	0.3421	0.4099	-0.0952	0.3501	-0.0653	0.0657	-0.0964	0.0179	-0.044	0.0285	0.3181	-0.0987	0.0223	0.2238	-0.0308	0.035	0.1287	-0.008	0.1785	16.6979	66.8211	34.6417
8	0.5138	-0.1566	-0.2186	0.3772	0.4403	0.8673	-0.0679	-0.0171	-0.0674	0.0401	-0.0203	0.0795	0.1715	-0.0421	-0.0012	0.1691	0.008	0.0297	0.1241	0.0138	0.1571	19.4694	72.5514	45.6658
9	0.0747	0.0372	-0.0166	0.0884	0.0714	0.0961	-0.0512	-0.1029	-0.074	0.1058	0.0348	0.054	0.1021	0.0719	-0	0.1804	0.0436	0.0139	0.1792	0.0243	0.1535	29.6977	75.2712	53.7751
10	0.0333	-0.0397	0.0005	0.0677	-0.0302	0.0424	0.0453	-0.0578	0.0708	0.0835	-0.0357	0.0483	-0.046	0.0154	-0	0.1777	0.0012	0.0177	0.169	-0.0062	0.1731	19.4948	88.4764	57.4932
11	0.282	0.2515	0.0287	0.2861	-0.0211	0.0785	0.052	-0.2715	-0.0029	0.1771	-0.05	0.0471	0.066	0.2094	0.0015	0.2068	0.0231	0.0025	0.2413	0.0146	0.1486	27.2404	82.3406	63.8736
12	0.0975	0.1072	-0.0071	0.1175	-0.0092	0.0979	0.0924	-0.0496	0.0438	-0.0287	-0.0385	0.0156	-0.1455	0.1241	-0	0.19	-0.0012	0.018	0.1638	0.0044	0.1674	28.0555	93.2504	46.8353
13	0.1447	-0.0846	-0.1643	0.1775	0.0656	0.1928	-0.0201	-0.0746	0.1277	0.0448	-0.0282	-0.1094	-0.1248	0.3079	0.0004	0.1738	-0.0244	-0.0237	0.2356	0.005	0.1617	36.1722	90.056	51.075
14	0.0612	-0.0336	-0.084	0.041	0.0194	0.1441	-0.0703	-0.0278	-0.0428	0.0187	0.0592	0.0493	0.005	0.1258	-0.0031	0.1493	0.0216	0.0067	0.1596	0.0115	0.1462	32.9212	79.9926	39.3469

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID -7 THROUGH 11 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 12 THROUGH 34 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 35 THROUGH 99 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 100 THROUGH 177 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 178 THROUGH 229 )
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 230 THROUGH 275 )
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 1 THROUGH 21 )
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESID 22 THROUGH 145 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 146 THROUGH 168 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 169 THROUGH 188 )
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 189 THROUGH 213 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 214 THROUGH 229 )
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 230 THROUGH 255 )
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESID 256 THROUGH 275 )

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