PDB-4jlw: Crystal structure of formaldehyde dehydrogenase from Pseudomonas ...

ID or keywords:

Entry

Database: PDB / ID: 4jlw

Title

Crystal structure of formaldehyde dehydrogenase from Pseudomonas aeruginosa

Components

Glutathione-independent formaldehyde dehydrogenase

Keywords

OXIDOREDUCTASE / Rossmann Fold / Zinc Finger / dehydrogenase / NAD+ Binding / Zinc Binding

Function / homology

Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / :

Function and homology information

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Chen, S. / Liao, Y.P. / Wang, D.L. / Wang, S. / Ding, J.F. / Wang, Y.M. / Cai, L.J. / Ran, X.Y. / Zhu, H.X.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of formaldehyde dehydrogenase from Pseudomonas aeruginosa: the binary complex with the cofactor NAD+.
Authors: Liao, Y.P. / Chen, S. / Wang, D.L. / Zhang, W. / Wang, S. / Ding, J.F. / Wang, Y.M. / Cai, L.J. / Ran, X.Y. / Wang, X. / Zhu, H.X.

History

Deposition	Mar 13, 2013	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Oct 30, 2013	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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.pdbx_dist_value / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _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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Download

PDBx/mmCIF format	4jlw.cif.gz	587.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4jlw.ent.gz	490 KB	Display	PDB format
PDBx/mmJSON format	4jlw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4jlw_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	4jlw_full_validation.pdf.gz	1.4 MB	Display
Data in XML	4jlw_validation.xml.gz	61.7 KB	Display
Data in CIF	4jlw_validation.cif.gz	84.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jl/4jlw ftp://data.pdbj.org/pub/pdb/validation_reports/jl/4jlw	HTTPS FTP

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Related structure data

Related structure data	1kolS S: Starting model for refinement
Similar structure data	1kol-1 2dph-1 1ykf-d 7jnq-d 4zic-2 6sch-d 4zic-1 6tj8-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#87 - Mar 2007 Zinc Fingers similarity (1)

Deposited unit

A: Glutathione-independent formaldehyde dehydrogenase

B: Glutathione-independent formaldehyde dehydrogenase

C: Glutathione-independent formaldehyde dehydrogenase

D: Glutathione-independent formaldehyde dehydrogenase

hetero molecules

172 kDa, 4 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)	89.226, 98.305, 99.623
Angle α, β, γ (deg.)	90.00, 91.29, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Glutathione-independent formaldehyde dehydrogenase Mass: 42057.039 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: LESB58 / Gene: fdhA, PLES_58161 / Plasmid: pCold II / Production host: Escherichia coli (E. coli) / Strain (production host): pG-Tf2 / References: UniProt: B7V5W2
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.6 Å³/Da / Density % sol: 52.63 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M Bis-Tris, 1.8M ammonium sulfate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2011
Radiation	Monochromator: DOUBLE CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 2.7→50 Å / Num. obs: 47323 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / R_merge(I) obs: 0.203 / Net I/σ(I): 6.43
Reflection shell	Resolution: 2.7→2.8 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.634 / Mean I/σ(I) obs: 2.91 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.6.0117	refinement
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1KOL

1kol

Resolution: 2.7→30 Å / Cor.coef. F_o:F_c: 0.907 / Cor.coef. F_o:F_c free: 0.865 / SU B: 28.45 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25936	2394	5.1 %	RANDOM
R_work	0.20926	-	-	-
obs	0.2118	44912	99.3 %	-

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: 27.159 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.05 Å²	-0 Å²	-0.37 Å²
2-	-	-2.27 Å²	-0 Å²
3-	-	-	-1.79 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11704	0	214	454	12372

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	12193
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.641	1.981	16580
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.53	5	1576
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.853	23.917	480
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.377	15	1880
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.482	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.105	0.2	1866
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	9208
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.696→2.765 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.369	171	-
R_work	0.272	2980	-
obs	-	-	92.98 %

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	1.6403	-0.3406	-0.1958	0.6172	0.9606	1.6044	0.0934	0.3206	0.2271	-0.1857	-0.0349	-0.0977	-0.258	0.0222	-0.0585	0.152	-0.0151	0.0507	0.1246	0.0879	0.1405	29.684	0.0349	3.7877
2	0.9815	-0.2874	-0.277	1.7496	-0.0897	1.3584	0.0352	-0.003	0.0096	0.0709	-0.0112	-0.1514	-0.1513	0.0264	-0.0241	0.1194	-0.041	-0.0368	0.023	0.0069	0.0899	27.7205	-6.2798	11.4657
3	1.3342	0.3688	-0.9607	4.0987	-0.0604	1.7359	-0.1193	0.1191	-0.2114	-0.0728	-0.0601	-0.162	0.2889	0.0712	0.1794	0.0584	0.0407	0.0282	0.1389	0	0.1158	37.4084	-31.6339	10.2378
4	0.9653	0.7523	-0.1831	1.3193	-0.3817	0.7838	0.0207	0.197	-0.0989	-0.239	0.0323	-0.3283	-0.0105	0.0779	-0.053	0.1344	0.0352	0.083	0.1581	0.0009	0.1475	31.7935	-20.9017	4.7467
5	1.6108	0.205	0.9504	0.584	-0.2384	2.6412	0.015	-0.0122	-0.0794	0.0236	0.0196	0.0568	0.3719	-0.1993	-0.0346	0.1874	0.01	0.027	0.0477	-0.0226	0.109	3.5923	-56.1655	17.9388
6	2.1573	0.1756	0.3169	1.2189	0.2776	1.8253	-0.0616	-0.1027	0.0161	0.0696	0.0129	0.0308	0.2182	0.0082	0.0487	0.181	-0.0216	0.0336	0.0178	0.0068	0.0381	5.7047	-48.9167	22.321
7	0.4975	0.5747	0.6555	2.7608	-0.6335	1.813	0.0291	-0.0244	0.043	-0.0633	-0.0118	0.1212	0.0857	-0.0821	-0.0173	0.0911	0.0016	0.0247	0.1132	-0.0176	0.0829	-3.1835	-26.9848	9.3718
8	0.6975	0.4485	0.1099	0.8037	-0.3808	0.81	0.0529	0.1523	-0.0161	-0.012	0.0566	0.1426	0.0303	-0.0019	-0.1095	0.1217	0.0233	-0.0466	0.0857	-0.0194	0.1049	5.9772	-33.0175	7.4858
9	8.868	2.9482	-5.0405	1.0077	-1.5893	3.959	0.0161	0.8388	0.4124	0.0784	0.2442	0.1901	0.3838	-1.2758	-0.2603	0.4283	-0.1799	0.0282	0.6986	0.0692	0.2157	-11.3282	-50.367	11.9161
10	1.5407	-0.4994	-0.1058	0.8911	-0.5141	3.575	0.0622	-0.1109	0.2757	0.0691	0.0151	-0.0859	-0.3548	-0.1386	-0.0773	0.2089	-0.0014	-0.0146	0.0358	-0.0526	0.1311	2.8134	8.9616	37.1451
11	2.6275	-1.7821	0.5019	2.0838	-0.5032	2.143	-0.0399	-0.0135	-0.0456	0.116	0.0984	0.0416	-0.3934	0.0904	-0.0585	0.1484	-0.0104	-0.0204	0.0212	0.0202	0.0925	9.4338	3.4044	27.3084
12	9.425	0.7951	-1.416	3.5677	0.3347	4.0531	0.0098	0.6367	0.0912	-0.182	-0.0128	0.4056	-0.1282	-0.3749	0.003	0.1914	0.0395	-0.0126	0.0788	-0.0179	0.0842	-3.9699	-2.1255	20.6749
13	0.7483	-0.4648	-0.2144	3.4979	-0.5503	1.122	0.1066	-0.1039	-0.0851	0.0452	-0.0834	0.0813	0.066	-0.0329	-0.0232	0.1037	-0.0038	-0.0092	0.1094	-0.0151	0.0451	-3.7366	-21.3114	40.3278
14	0.7783	-0.5636	0.0969	1.1385	-0.2209	0.4164	0.087	-0.0646	0.0416	0.1091	-0.0142	0.1273	-0.0657	0.0894	-0.0728	0.1139	-0.0166	0.0362	0.134	-0.013	0.087	5.4657	-15.3756	42.5822
15	1.7088	-0.1485	0.5931	6.0443	-1.6585	6.6791	-0.1311	0.0576	-0.1565	0.1243	-0.0308	0.2667	-0.2559	-0.5899	0.1619	0.0859	0.0386	0.0791	0.1407	-0.0341	0.1217	-11.4654	2.1767	37.4268
16	1.689	0.0529	0.1328	0.9884	0.5707	1.5838	0.09	-0.1822	-0.0875	0.2301	-0.0645	-0.1199	0.2288	0.0277	-0.0255	0.1525	-0.0143	-0.016	0.0615	0.0525	0.0952	26.12	-47.3293	46.0892
17	0.71	0.9663	0.124	2.5875	-1.1162	1.3416	0.0336	-0.015	-0.0615	-0.0246	-0.0424	-0.1225	0.0904	0.07	0.0088	0.0833	0.036	-0.0304	0.1286	0.0052	0.14	30.967	-43.1662	39.2337
18	0.977	0.6391	0.0886	0.8422	0.0214	1.467	-0.0172	-0.015	0.1056	0.2506	-0.0494	-0.0768	-0.137	0.1991	0.0665	0.1838	-0.0233	-0.0625	0.105	0.0302	0.1536	34.9457	-17.2898	44.5528
19	0.6433	-0.8224	0.0226	1.9204	-0.0919	1.0635	0.0241	-0.0418	-0.0449	0.222	-0.0144	-0.1779	-0.0365	0.1374	-0.0097	0.0904	-0.0566	-0.0843	0.112	0.0129	0.1491	31.2828	-30.4771	44.4644

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 101
2	X-RAY DIFFRACTION	2	A	102 - 181
3	X-RAY DIFFRACTION	3	A	182 - 261
4	X-RAY DIFFRACTION	4	A	262 - 397
5	X-RAY DIFFRACTION	5	B	3 - 101
6	X-RAY DIFFRACTION	6	B	102 - 168
7	X-RAY DIFFRACTION	7	B	169 - 261
8	X-RAY DIFFRACTION	8	B	262 - 363
9	X-RAY DIFFRACTION	9	B	364 - 397
10	X-RAY DIFFRACTION	10	C	3 - 69
11	X-RAY DIFFRACTION	11	C	70 - 144
12	X-RAY DIFFRACTION	12	C	145 - 168
13	X-RAY DIFFRACTION	13	C	169 - 261
14	X-RAY DIFFRACTION	14	C	262 - 363
15	X-RAY DIFFRACTION	15	C	364 - 397
16	X-RAY DIFFRACTION	16	D	3 - 120
17	X-RAY DIFFRACTION	17	D	121 - 181
18	X-RAY DIFFRACTION	18	D	182 - 290
19	X-RAY DIFFRACTION	19	D	291 - 397

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