PDB-5hfn: Crystal structure of a loop truncation variant of Thermotoga mari...

ID or keywords:

Entry

Database: PDB / ID: 5hfn

Title

Crystal structure of a loop truncation variant of Thermotoga maritima Acetyl Esterase TM0077 (apo structure) at 2.75 Angstrom resolution

Components

Cephalosporin-C deacetylase

Keywords

HYDROLASE /

carbohydrate metabolism / cephalosporin C deacetylase /

Rossmann fold

Function / homology

Function and homology information

xylan metabolic process / cephalosporin C metabolic process /

cephalosporin-C deacetylase /

cephalosporin-C deacetylase activity / polysaccharide metabolic process /

acetylxylan esterase /

acetylxylan esterase activity /

carboxylic ester hydrolase activity / cellulose catabolic process /

calcium ion binding /

cytoplasm
Similarity search - Function

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Manoj, N. / Singh, M.K.

Funding support

India, 1items

Citation

Journal: J.Struct.Biol. / Year: 2016
Title: An extended loop in CE7 carbohydrate esterase family is dispensable for oligomerization but required for activity and thermostability
Authors: Singh, M.K. / Manoj, N.

History

Deposition	Jan 7, 2016	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	May 25, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5hfn.cif.gz	666.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5hfn.ent.gz	553.5 KB	Display	PDB format
PDBx/mmJSON format	5hfn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hf/5hfn ftp://data.pdbj.org/pub/pdb/validation_reports/hf/5hfn	HTTPS FTP

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Related structure data

Related structure data	5fdfSC 1vlq 3m81 3m82 3m83 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5jib-d 6fkx-d 3m81-d 6agq-d 3fcy-1 5gma-d 3m82-d 3dky-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Cephalosporin-C deacetylase

B: Cephalosporin-C deacetylase

C: Cephalosporin-C deacetylase

D: Cephalosporin-C deacetylase

E: Cephalosporin-C deacetylase

F: Cephalosporin-C deacetylase

215 kDa, 6 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)	155.080, 155.080, 165.100
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	PHE	PHE	GLU	GLU	A	A	4 - 323	16 - 309
2	1	PHE	PHE	GLU	GLU	B	B	4 - 323	16 - 309
1	2	PHE	PHE	GLU	GLU	A	A	3 - 323	15 - 309
2	2	PHE	PHE	GLU	GLU	C	C	3 - 323	15 - 309
1	3	ALA	ALA	PHE	PHE	A	A	2 - 322	14 - 308
2	3	ALA	ALA	PHE	PHE	D	D	2 - 322	14 - 308
1	4	ALA	ALA	GLU	GLU	A	A	2 - 323	14 - 309
2	4	ALA	ALA	GLU	GLU	E	E	2 - 323	14 - 309
1	5	PHE	PHE	PHE	PHE	A	A	4 - 322	16 - 308
2	5	PHE	PHE	PHE	PHE	F	F	4 - 322	16 - 308
1	6	PHE	PHE	PHE	PHE	B	B	4 - 322	16 - 308
2	6	PHE	PHE	PHE	PHE	C	C	4 - 322	16 - 308
1	7	PHE	PHE	PHE	PHE	B	B	4 - 322	16 - 308
2	7	PHE	PHE	PHE	PHE	D	D	4 - 322	16 - 308
1	8	PHE	PHE	PHE	PHE	B	B	4 - 322	16 - 308
2	8	PHE	PHE	PHE	PHE	E	E	4 - 322	16 - 308
1	9	PHE	PHE	GLU	GLU	B	B	4 - 323	16 - 309
2	9	PHE	PHE	GLU	GLU	F	F	4 - 323	16 - 309
1	10	PHE	PHE	PHE	PHE	C	C	4 - 322	16 - 308
2	10	PHE	PHE	PHE	PHE	D	D	4 - 322	16 - 308
1	11	PHE	PHE	GLU	GLU	C	C	4 - 323	16 - 309
2	11	PHE	PHE	GLU	GLU	E	E	4 - 323	16 - 309
1	12	PHE	PHE	GLU	GLU	C	C	4 - 323	16 - 309
2	12	PHE	PHE	GLU	GLU	F	F	4 - 323	16 - 309
1	13	ALA	ALA	PHE	PHE	D	D	2 - 322	14 - 308
2	13	ALA	ALA	PHE	PHE	E	E	2 - 322	14 - 308
1	14	PHE	PHE	PHE	PHE	D	D	4 - 322	16 - 308
2	14	PHE	PHE	PHE	PHE	F	F	4 - 322	16 - 308
1	15	PHE	PHE	GLU	GLU	E	E	4 - 323	16 - 309
2	15	PHE	PHE	GLU	GLU	F	F	4 - 323	16 - 309

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	Cephalosporin-C deacetylase / / Acetylxylan esterase Mass: 35840.891 Da / Num. of mol.: 6 / Mutation: Deletion of residues 120-145 Source method: isolated from a genetically manipulated source Details: The crystallized construct is a truncated mutant containing a deletion of residue numbers 120-145 of the full length protein. Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: axeA, TM_0077 / Plasmid: PMH1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL References: UniProt: Q9WXT2, cephalosporin-C deacetylase, acetylxylan esterase
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Cephalosporin-C deacetylase /

/ Acetylxylan esterase

Mass: 35840.891 Da / Num. of mol.: 6 / Mutation: Deletion of residues 120-145
Source method: isolated from a genetically manipulated source
Details: The crystallized construct is a truncated mutant containing a deletion of residue numbers 120-145 of the full length protein.
Source: (gene. exp.)

Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: axeA, TM_0077 / Plasmid: PMH1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL
References: UniProt: Q9WXT2,

cephalosporin-C deacetylase,

acetylxylan esterase

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.67 Å³/Da / Density % sol: 53.85 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Reservoir solution is composed of 35%(V/V) Pentaerythritolpropoxylate (5/4 PO/OH), 200mM potassium chloride, 50mM HEPES pH 7.5

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å

Detector

Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 16, 2013

Radiation

Monochromator: Double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2.75→52.09 Å / Num. obs: 60062 / % possible obs: 100 % / Redundancy: 10.5 % / B_iso Wilson estimate: 62.65 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.145 / R_pim(I) all: 0.046 / Net I/σ(I): 14.7 / Num. measured all: 632921 / Scaling rejects: 87

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	CC_1/2	R_pim(I) all	% possible all
2.75-2.82	8.9	1.174	2.2	39151	4413	0.716	0.408	100
12.3-52.09	11	0.035	41	8276	755	0.993	0.012	98.9

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Processing

Software

Name	Version	Classification
MAR345dtb		data collection
Aimless	0.1.30	data scaling
REFMAC	5	refinement
PDB_EXTRACT	3.15	data extraction
MOSFLM		data reduction
MOLREP		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5FDF

5fdf

Resolution: 2.75→52.09 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.917 / SU B: 27.666 / SU ML: 0.25 / SU R Cruickshank DPI: 0.2989 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.061 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2306	3028	5 %	RANDOM
R_work	0.1981	-	-	-
obs	0.1997	56965	99.92 %	-

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 max: 116.56 Å² / B_iso mean: 53.878 Å² / B_iso min: 14 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.44 Å²	-0.22 Å²	-0 Å²
2-	-	-0.44 Å²	0 Å²
3-	-	-	1.43 Å²

Refine analyze

Luzzati coordinate error obs: 0.3912 Å / Luzzati d res low obs: 5 Å

Refinement step

Cycle: final / Resolution: 2.75→52.09 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13211	0	0	85	13296
B_iso mean	-	-	-	32.89	-
Num. residues	-	-	-	-	1678

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.019	13636
X-RAY DIFFRACTION	r_bond_other_d	0.012	0.02	12720
X-RAY DIFFRACTION	r_angle_refined_deg	1.816	1.946	18540
X-RAY DIFFRACTION	r_angle_other_deg	1.677	3	29182
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.397	5	1670
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.734	23.087	635
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.752	15	2039
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.42	15	78
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	1980
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.021	15514
X-RAY DIFFRACTION	r_gen_planes_other	0.011	0.02	3354
X-RAY DIFFRACTION	r_mcbond_it	1.087	1.916	6704
X-RAY DIFFRACTION	r_mcbond_other	1.085	1.915	6703
X-RAY DIFFRACTION	r_mcangle_it	1.825	2.865	8351

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	32424	0.07
1	2	B	32424	0.07
2	1	A	32372	0.06
2	2	C	32372	0.06
3	1	A	32444	0.06
3	2	D	32444	0.06
4	1	A	33312	0.05
4	2	E	33312	0.05
5	1	A	32582	0.07
5	2	F	32582	0.07
6	1	B	32440	0.07
6	2	C	32440	0.07
7	1	B	32068	0.06
7	2	D	32068	0.06
8	1	B	32784	0.06
8	2	E	32784	0.06
9	1	B	32672	0.08
9	2	F	32672	0.08
10	1	C	32678	0.05
10	2	D	32678	0.05
11	1	C	32790	0.05
11	2	E	32790	0.05
12	1	C	33190	0.06
12	2	F	33190	0.06
13	1	D	32940	0.05
13	2	E	32940	0.05
14	1	D	32938	0.06
14	2	F	32938	0.06
15	1	E	33112	0.06
15	2	F	33112	0.06

LS refinement shell

Resolution: 2.75→2.821 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.317	237	-
R_work	0.302	4168	-
all	-	4405	-
obs	-	-	99.89 %

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)	Details	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	5.6376	0.7138	2.6642	1.7166	0.1785	1.8778	-0.0334	-1.048	0.189	0.4013	0.0975	-0.104	-0.0728	-0.5666	-0.0641	0.2646	0.0795	-0.0021	0.3301	0.0017	0.3776	Chain A group 1	45.5522	120.2026	47.1507
2	3.2191	-0.343	-0.3878	1.1985	0.0712	2.1247	-0.065	-0.0318	-0.1067	-0.0089	0.1206	0.0966	0.0791	-0.149	-0.0557	0.1239	0.0312	-0.0424	0.211	0.0845	0.3277	Chain A group 2	39.9091	111.375	36.5525
3	1.335	0.2281	-0.5346	1.3203	0.3018	2.9788	-0.0443	0.205	-0.1122	-0.0624	-0.0479	0.3546	0.2687	0.0876	0.0922	0.146	0.0032	-0.0132	0.2376	-0.0048	0.6028	Chain B group 1	13.8362	67.5308	43.9186
4	0.9562	-0.1383	-0.6355	2.7111	0.3803	2.0297	0.123	0.3612	-0.067	-0.3448	-0.1446	0.3312	-0.116	-0.1712	0.0216	0.121	0.008	-0.1331	0.2783	0.0814	0.4562	Chain B group 2	18.3204	74.858	35.1757
5	1.5196	-0.2161	0.0406	5.8177	-1.0369	1.6353	-0.0588	0.3461	0.0167	-0.5706	-0.0067	-1.069	-0.3156	0.4234	0.0656	0.4057	-0.1199	0.1886	0.4874	-0.0523	0.4562	Chain C group 1	67.884	71.3182	14.5223
6	2.2913	0.6695	0.2528	4.0623	0.4091	0.7759	-0.0733	0.2949	0.2393	-0.6999	0.1777	0.0665	-0.2538	0.0958	-0.1044	0.4236	-0.0355	0.0139	0.3446	0.0615	0.2889	Chain C group 2	54.4838	80.7255	15.6555
7	4.7424	0.5939	1.2781	2.0752	0.1312	2.3104	-0.0782	-0.2976	0.6349	0.3756	-0.0032	0.4292	-0.6335	-0.0983	0.0814	0.5167	0.0155	0.188	0.2017	-0.1226	0.4302	Chain D group 1	23.6133	90.7205	69.8409
8	3.6504	0.9938	-0.169	2.9702	0.01	1.0985	0.1946	-0.4036	0.2254	0.6196	-0.0873	-0.0291	-0.1723	0.2005	-0.1073	0.358	0.0061	0.0124	0.2241	-0.0861	0.2189	Chain D group 2	37.6525	85.3454	69.4939
9	1.6842	0.0289	-0.8085	2.5643	1.1203	3.0471	-0.1459	0.1257	-0.1462	0.0955	0.0368	0.0201	0.0527	-0.2212	0.1091	0.163	0.0311	0.0438	0.1335	-0.0643	0.4208	Chain E group 1	51.1346	47.2624	36.7017
10	2.1485	0.2432	-0.799	2.2013	0.6123	2.3263	-0.1254	-0.1834	-0.1013	0.4034	0.1189	-0.065	0.1328	0.0932	0.0065	0.1767	0.056	-0.0573	0.1675	-0.0747	0.3014	Chain E group 2	53.7751	57.054	48.762
11	2.3431	-1.4854	0.3397	4.7694	-0.7909	0.9753	0.1124	0.3969	0.2843	-0.3606	-0.2175	-0.6907	0.0597	0.1763	0.1051	0.1254	-0.0068	-0.0081	0.2253	-0.0128	0.5696	Chain F group 1	78.0523	102.2749	43.9816
12	1.9885	-1.1477	-0.5056	3.0762	0.4062	2.0695	-0.1418	0.0323	-0.112	0.3627	0.0173	-0.1401	0.1184	-0.0529	0.1245	0.1107	0.0076	-0.0743	0.1388	0.0096	0.4059	Chain F group 2	71.0864	90.6681	52.4644

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 178
2	X-RAY DIFFRACTION	2	A	179 - 323
3	X-RAY DIFFRACTION	3	B	4 - 158
4	X-RAY DIFFRACTION	4	B	159 - 323
5	X-RAY DIFFRACTION	5	C	3 - 189
6	X-RAY DIFFRACTION	6	C	190 - 323
7	X-RAY DIFFRACTION	7	D	-2 - 189
8	X-RAY DIFFRACTION	8	D	190 - 323
9	X-RAY DIFFRACTION	9	E	2 - 189
10	X-RAY DIFFRACTION	10	E	190 - 323
11	X-RAY DIFFRACTION	11	F	4 - 218
12	X-RAY DIFFRACTION	12	F	219 - 323

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Yorodumi