PDB-2f4l: Crystal structure of a putative acetamidase (tm0119) from thermot...

ID or keywords:

Entry

Database: PDB / ID: 2f4l

Title

Crystal structure of a putative acetamidase (tm0119) from thermotoga maritima msb8 at 2.50 A resolution

Components

acetamidase, putative

Keywords

HYDROLASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2

Function / homology

Function and homology information

hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / metal ion binding
Similarity search - Function

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.5 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: To be published
Title: Crystal structure of Acetamidase, putative (tm0119) from THERMOTOGA MARITIMA at 2.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Nov 23, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 6, 2005	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	Jan 25, 2023	Group: Database references / Derived calculations Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Nov 20, 2024	Group: Data collection / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2f4l.cif.gz	226.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2f4l.ent.gz	179.8 KB	Display	PDB format
PDBx/mmJSON format	2f4l.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2f4l_validation.pdf.gz	467.6 KB	Display	wwPDB validaton report
Full document	2f4l_full_validation.pdf.gz	478.4 KB	Display
Data in XML	2f4l_validation.xml.gz	39.7 KB	Display
Data in CIF	2f4l_validation.cif.gz	55.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f4/2f4l ftp://data.pdbj.org/pub/pdb/validation_reports/f4/2f4l	HTTPS FTP

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Related structure data

Similar structure data	5bvi-d 2o11-d 6i4m-d 1i3r-3 5on0-1 3utw-2 2fwr-3 1i3r-5 1t44-d 1a8k-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
Other databases	TargetDB: 282000

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: acetamidase, putative

B: acetamidase, putative

C: acetamidase, putative

D: acetamidase, putative

hetero molecules

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

1

A: acetamidase, putative

B: acetamidase, putative

hetero molecules

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

2

C: acetamidase, putative

D: acetamidase, putative

hetero molecules

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

Unit cell

Length a, b, c (Å)	80.257, 104.068, 154.945
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Refine code: 4

Dom-ID	Component-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	1	MSE	MSE	ASP	ASP	A	A	1 - 35	13 - 47
2	1	1	MSE	MSE	ASP	ASP	B	B	1 - 35	13 - 47
3	1	1	MSE	MSE	ASP	ASP	C	C	1 - 35	13 - 47
4	1	1	MSE	MSE	ASP	ASP	D	D	1 - 35	13 - 47
5	2	1	VAL	VAL	GLN	GLN	A	A	49 - 164	61 - 176
6	2	1	VAL	VAL	GLN	GLN	B	B	49 - 164	61 - 176
7	2	1	VAL	VAL	GLN	GLN	C	C	49 - 164	61 - 176
8	2	1	VAL	VAL	GLN	GLN	D	D	49 - 164	61 - 176
9	3	1	MSE	MSE	GLN	GLN	A	A	122 - 164	134 - 176
10	3	1	MSE	MSE	GLN	GLN	B	B	122 - 164	134 - 176
11	3	1	MSE	MSE	GLN	GLN	C	C	122 - 164	134 - 176
12	3	1	MSE	MSE	GLN	GLN	D	D	122 - 164	134 - 176
13	4	1	LEU	LEU	HIS	HIS	A	A	169 - 175	181 - 187
14	4	1	LEU	LEU	HIS	HIS	B	B	169 - 175	181 - 187
15	4	1	LEU	LEU	HIS	HIS	C	C	169 - 175	181 - 187
16	4	1	LEU	LEU	HIS	HIS	D	D	169 - 175	181 - 187
1	1	2	LEU	LEU	VAL	VAL	A	A	76 - 90	88 - 102
2	1	2	LEU	LEU	VAL	VAL	B	B	76 - 90	88 - 102
3	1	2	LEU	LEU	VAL	VAL	C	C	76 - 90	88 - 102
4	1	2	LEU	LEU	VAL	VAL	D	D	76 - 90	88 - 102
5	2	2	GLU	GLU	PRO	PRO	A	A	96 - 121	108 - 133
6	2	2	GLU	GLU	PRO	PRO	B	B	96 - 121	108 - 133
7	2	2	GLU	GLU	PRO	PRO	C	C	96 - 121	108 - 133
8	2	2	GLU	GLU	PRO	PRO	D	D	96 - 121	108 - 133
9	3	2	PRO	PRO	GLU	GLU	A	A	191 - 203	203 - 215
10	3	2	PRO	PRO	GLU	GLU	B	B	191 - 203	203 - 215
11	3	2	PRO	PRO	GLU	GLU	C	C	191 - 203	203 - 215
12	3	2	PRO	PRO	GLU	GLU	D	D	191 - 203	203 - 215
1	1	3	GLU	GLU	THR	THR	A	A	203 - 283	215 - 295
2	1	3	GLU	GLU	THR	THR	B	B	203 - 283	215 - 295
3	1	3	GLU	GLU	THR	THR	C	C	203 - 283	215 - 295
4	1	3	GLU	GLU	THR	THR	D	D	203 - 283	215 - 295

NCS ensembles :

ID
1
2
3

#1: Protein	acetamidase, putative Mass: 33067.691 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm0119 / Plasmid: HK100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WXX3
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.44 Å³/Da / Density % sol: 54.16 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5 Details: 10.0% Glycerol, 5.0% PEG-3000, 30.0% PEG-400, 0.1M Citrate, pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.89194, 0.97936

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 12, 2005

Radiation

Monochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.89194	1
2	0.97936	1

Reflection

Resolution: 2.5→29.7 Å / Num. obs: 45660 / % possible obs: 99.9 % / Redundancy: 3.7 % / R_merge(I) obs: 0.137 / R_sym value: 0.137 / Net I/σ(I): 4.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	% possible obs (%)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	R_sym value
2.5-2.56	100	3.7	0.923	0.7	3344	0.923
2.56-2.64	100	3.7	0.732	0.9	3226	0.732
2.64-2.71	100	3.7	0.603	1.2	3157	0.603
2.71-2.8	100	3.7	0.518	1.4	3081	0.518
2.8-2.89	100	3.7	0.442	1.6	2982	0.442
2.89-2.99	100	3.7	0.35	2.1	2904	0.35
2.99-3.1	100	3.7	0.277	2.2	2760	0.277
3.1-3.23	100	3.7	0.201	3.7	2707	0.201
3.23-3.37	100	3.7	0.165	4.5	2595	0.165
3.37-3.54	100	3.7	0.138	5.3	2454	0.138
3.54-3.73	100	3.7	0.116	6.2	2360	0.116
3.73-3.95	100	3.6	0.096	6.8	2220	0.096
3.95-4.23	100	3.6	0.078	7.8	2132	0.078
4.23-4.56	100	3.6	0.062	9.9	1970	0.062
4.56-5	100	3.6	0.056	10.6	1816	0.056
5-5.59	100	3.6	0.063	10.2	1651	0.063
5.59-6.45	100	3.6	0.068	9.2	1485	0.068
6.45-7.91	99.9	3.5	0.054	11.4	1256	0.054
7.91-11.18	99.8	3.4	0.042	13	1009	0.042
11.18-29.7	94.1	3.2	0.042	11.5	551	0.042

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
SCALA		data scaling
PDB_EXTRACT	1.601	data extraction
MOSFLM		data reduction
CCP4	(SCALA)	data scaling
SHELXE		model building
SHARP		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.5→29.7 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.915 / SU B: 18.972 / SU ML: 0.201 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.472 / ESU R Free: 0.273
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.242	2305	5.1 %	RANDOM
R_work	0.192	-	-	-
all	0.194	-	-	-
obs	-	43287	99.85 %	-

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: 23.323 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.1 Å²	0 Å²	0 Å²
2-	-	-2.24 Å²	0 Å²
3-	-	-	2.34 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→29.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8355	0	10	163	8528

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	8556
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	5691
X-RAY DIFFRACTION	r_angle_refined_deg	1.269	1.966	11657
X-RAY DIFFRACTION	r_angle_other_deg	0.839	3	13997
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.451	5	1098
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.082	24.198	324
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.02	15	1409
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.495	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	1375
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	9427
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1611
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	1471
X-RAY DIFFRACTION	r_nbd_other	0.184	0.2	5734
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	4166
X-RAY DIFFRACTION	r_nbtor_other	0.084	0.2	4590
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.15	0.2	229
X-RAY DIFFRACTION	r_metal_ion_refined	0.002	0.2	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.107	0.2	16
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.269	0.2	46
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.128	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	1.298	3	5838
X-RAY DIFFRACTION	r_mcbond_other	0.298	3	2219
X-RAY DIFFRACTION	r_mcangle_it	1.901	5	8941
X-RAY DIFFRACTION	r_scbond_it	3.942	8	3342
X-RAY DIFFRACTION	r_scangle_it	5.606	11	2713

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	2473	MEDIUM POSITIONAL	0.33	0.5
1	2	B	2473	MEDIUM POSITIONAL	0.35	0.5
1	3	C	2473	MEDIUM POSITIONAL	0.3	0.5
1	4	D	2473	MEDIUM POSITIONAL	0.35	0.5
1	1	A	2473	MEDIUM THERMAL	0.44	2
1	2	B	2473	MEDIUM THERMAL	0.4	2
1	3	C	2473	MEDIUM THERMAL	0.4	2
1	4	D	2473	MEDIUM THERMAL	0.38	2
2	1	A	682	MEDIUM POSITIONAL	0.22	0.5
2	2	B	682	MEDIUM POSITIONAL	0.22	0.5
2	3	C	682	MEDIUM POSITIONAL	0.32	0.5
2	4	D	682	MEDIUM POSITIONAL	0.24	0.5
2	1	A	682	MEDIUM THERMAL	0.34	2
2	2	B	682	MEDIUM THERMAL	0.36	2
2	3	C	682	MEDIUM THERMAL	0.35	2
2	4	D	682	MEDIUM THERMAL	0.35	2
3	1	A	1069	MEDIUM POSITIONAL	0.23	0.5
3	2	B	1069	MEDIUM POSITIONAL	0.33	0.5
3	3	C	1069	MEDIUM POSITIONAL	0.25	0.5
3	4	D	1069	MEDIUM POSITIONAL	0.26	0.5
3	1	A	1069	MEDIUM THERMAL	0.53	2
3	2	B	1069	MEDIUM THERMAL	0.48	2
3	3	C	1069	MEDIUM THERMAL	0.5	2
3	4	D	1069	MEDIUM THERMAL	0.47	2

LS refinement shell

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

	R_factor	Num. reflection	% reflection
R_free	0.34	183	-
R_work	0.303	3141	-
obs	-	-	99.43 %

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	3.4374	-1.3651	-0.5273	3.6542	0.7186	2.1574	-0.0845	-0.1255	0.1348	0.2934	0.1148	-0.1218	-0.0849	-0.0143	-0.0303	0.0469	-0.0248	-0.0147	-0.0292	0.0195	-0.0343	25.108	80.515	61.337
2	0.7137	0.3797	-0.0164	1.4469	-0.1763	0.9175	-0.0052	-0.0293	-0.0127	0.083	-0.0039	-0.0908	-0.0125	0.0276	0.0092	0.0031	0.0184	-0.0212	-0.0012	-0.011	-0.0855	23.327	64.294	60.328
3	5.0209	-1.7399	0.511	4.2574	-0.9531	1.7101	-0.197	-0.2917	-0.1658	0.124	0.2538	-0.0157	0.0919	-0.0652	-0.0568	0.0337	-0.0197	0.0229	-0.0135	-0.0133	-0.059	14.46	27.61	62.166
4	0.9976	0.3165	0.1714	1.5999	-0.1972	0.8317	-0.0848	0.0222	0.0228	-0.0643	0.0592	0.1034	0.1141	-0.0314	0.0256	0.031	0.0002	0.0053	-0.0024	0.0172	-0.0708	15.489	39.787	58.001
5	3.8537	0.4261	-0.3843	3.3097	1.1719	2.0601	-0.0384	0.071	-0.1734	-0.0936	0.0805	-0.1672	-0.0063	0.1583	-0.0421	-0.0181	-0.0332	-0.0085	0.0403	0.0125	-0.049	46.249	58.996	103.147
6	1.4016	0.9133	0.1231	1.3884	0.1756	0.8508	0.0354	-0.0207	0.0652	0.0271	-0.0482	0.0521	-0.038	0.0282	0.0128	0.0073	-0.0067	0.0098	-0.0045	0.0115	-0.0745	32.741	55.358	104.518
7	5.1211	0.1022	0.8163	2.9161	-1.1617	2.1419	-0.0599	0.2399	0.3009	-0.0821	0.0942	0.3844	0.0812	-0.2052	-0.0343	0.0204	-0.0214	-0.0463	0.0386	-0.0032	0.0176	-4.032	41.13	100.59
8	1.4703	0.7728	-0.1706	1.3205	-0.1074	0.7765	-0.0157	-0.0085	0.0543	-0.0017	-0.0046	0.1613	0.0207	-0.0314	0.0204	0.0214	-0.0029	-0.0193	0.024	-0.0045	-0.0425	8.94	44.827	104.372

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: all

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	1 - 81	13 - 93
2	2	A	A	82 - 283	94 - 295
3	3	B	B	0 - 81	12 - 93
4	4	B	B	82 - 283	94 - 295
5	5	C	C	0 - 81	12 - 93
6	6	C	C	82 - 283	94 - 295
7	7	D	D	0 - 81	12 - 93
8	8	D	D	82 - 283	94 - 295

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-Movie

-Structure viewers

+Viewer log

-This page

-This web site

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+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi