PDB-1vl6: Crystal structure of NAD-dependent malic enzyme (TM0542) from The...

ID or keywords:

Entry

Database: PDB / ID: 1vl6

Title

Crystal structure of NAD-dependent malic enzyme (TM0542) from Thermotoga maritima at 2.61 A resolution

Components

malate oxidoreductase

Keywords

OXIDOREDUCTASE / TM0542 / NAD-DEPENDENT MALIC ENZYME / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics

Function / homology

Function and homology information

malate dehydrogenase (decarboxylating) (NADP+) activity / NAD binding / metal ion binding
Similarity search - Function

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.61 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: To be published
Title: Crystal structure of NAD-dependent malic enzyme (TM0542) from Thermotoga maritima at 2.61 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Jul 13, 2004	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 17, 2004	Provider: repository / Type: Initial release
Revision 1.1	Apr 26, 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 / struct_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4	Oct 9, 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

Remark 999

SEQUENCE FOR THE VAL/MET CONFLICT AT RESIDUE 1: THIS GENE PRODUCT WAS EXPRESSED AS A FUSION ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1vl6.cif.gz	285.3 KB	Display	PDBx/mmCIF format
PDB format	pdb1vl6.ent.gz	230.8 KB	Display	PDB format
PDBx/mmJSON format	1vl6.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/vl/1vl6 ftp://data.pdbj.org/pub/pdb/validation_reports/vl/1vl6	HTTPS FTP

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Related structure data

Similar structure data	20079 1rdf-4 2vpf-d 30410 5bp4-9 20470 30411 4eei-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
Other databases	TargetDB: 282415

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: malate oxidoreductase

B: malate oxidoreductase

C: malate oxidoreductase

D: malate oxidoreductase

171 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)	143.963, 143.963, 163.428
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Refine code: 3

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	ASP	ASP	GLN	GLN	A	A	2 - 156	14 - 168
2	1	ASP	ASP	GLN	GLN	B	B	2 - 156	14 - 168
3	1	ASP	ASP	GLN	GLN	C	C	2 - 156	14 - 168
4	1	ASP	ASP	GLN	GLN	D	D	2 - 156	14 - 168
1	2	GLN	GLN	GLU	GLU	A	A	157 - 175	169 - 187
2	2	GLN	GLN	GLU	GLU	B	B	157 - 175	169 - 187
3	2	GLN	GLN	GLU	GLU	C	C	157 - 175	169 - 187
4	2	GLN	GLN	GLU	GLU	D	D	157 - 175	169 - 187
1	3	LYS	LYS	VAL	VAL	A	A	176 - 185	188 - 197
2	3	LYS	LYS	VAL	VAL	C	C	176 - 185	188 - 197
3	3	LYS	LYS	VAL	VAL	D	D	176 - 185	188 - 197
1	4	ASN	ASN	ILE	ILE	A	A	186 - 235	198 - 247
2	4	ASN	ASN	ILE	ILE	B	B	186 - 235	198 - 247
3	4	ASN	ASN	ILE	ILE	C	C	186 - 235	198 - 247
1	5	THR	THR	ASN	ASN	A	A	236 - 310	248 - 322
2	5	THR	THR	ASN	ASN	C	C	236 - 310	248 - 322
3	5	THR	THR	ASN	ASN	D	D	236 - 310	248 - 322
1	6	GLN	GLN	SER	SER	A	A	311 - 375	323 - 387
2	6	GLN	GLN	SER	SER	B	B	311 - 375	323 - 387
3	6	GLN	GLN	SER	SER	C	C	311 - 375	323 - 387
4	6	GLN	GLN	SER	SER	D	D	311 - 375	323 - 387

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	malate oxidoreductase Mass: 42835.117 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM0542 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZ12
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 44 / 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: 2

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	2.85	56.87
2	3.12	60.31

Crystal grow

Temperature (K)	Crystal-ID	Method	Details
277	1	vapor diffusion, sitting drop, nanodrop	0.025M Citric Acid, 0.075M Citrate_Na3, 6.00% NP_Peg 6000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
277	2	vapor diffusion, sitting drop, nanodrop	0.025M Citric Acid, 0.075M Citrate_Na3, 6.00% NP_Peg 6000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
1,2		1

Diffraction source

Source	Site	Beamline	ID	Wavelength	Wavelength (Å)
SYNCHROTRON	ALS	8.3.1	1	1.11587
SYNCHROTRON	ALS	8.3.1	2		1.019943, 0.979762, 0.979619

Detector

Type: ADSC / Detector: CCD / Date: Jul 25, 2003

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Double Crystal Si(111)	SINGLE WAVELENGTH	M	x-ray	1
2		MAD	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.11587	1
2	1.019943	1
3	0.979762	1
4	0.979619	1

Reflection

Resolution: 2.6→47.12 Å / Num. obs: 57871 / % possible obs: 98.84 % / Redundancy: 3.26 % / B_iso Wilson estimate: 74.19 Å² / R_merge(I) obs: 0.054 / Net I/σ(I): 16.77

Reflection shell

Resolution: 2.6→2.69 Å / Redundancy: 2.86 % / R_merge(I) obs: 0.551 / Mean I/σ(I) obs: 1.84 / Num. unique all: 5591 / % possible all: 96.26

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Processing

Software

Name	Version	Classification
DENZO		data reduction
MOSFLM		data reduction
SCALEPACK		data scaling
SOLVE		phasing
SHARP		phasing
REFMAC	5.2.0003	refinement

Refinement

Method to determine structure:

MAD / Resolution: 2.61→47.12 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.941 / SU B: 23.972 / SU ML: 0.225 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.524 / ESU R Free: 0.286
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE ELECTRON DENSITY IN THE REGIONS OF B243-B254, B267-B268 AND B287-B306 ARE POOR, BUT THE DENSITY STILL SHOW CLEARLY THE MAIN CHAIN ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23929	2333	4.1 %	RANDOM
R_work	0.19189	-	-	-
obs	0.1938	55267	98.53 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 61.902 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.1 Å²	0.55 Å²	0 Å²
2-	-	1.1 Å²	0 Å²
3-	-	-	-1.64 Å²

Refinement step

Cycle: LAST / Resolution: 2.61→47.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11096	0	0	44	11140

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	11343
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	10623
X-RAY DIFFRACTION	r_angle_refined_deg	1.658	1.961	15422
X-RAY DIFFRACTION	r_angle_other_deg	0.933	3	24642
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.65	5	1486
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.556	25.045	448
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.945	15	1862
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.668	15	50
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	1810
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	12724
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2119
X-RAY DIFFRACTION	r_nbd_refined	0.236	0.2	2569
X-RAY DIFFRACTION	r_nbd_other	0.179	0.2	11098
X-RAY DIFFRACTION	r_nbtor_other	0.091	0.2	7174
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.15	0.2	248
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.4	0.2	17
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.274	0.2	36
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.094	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	1.521	3	7552
X-RAY DIFFRACTION	r_mcbond_other	0.492	3	3009
X-RAY DIFFRACTION	r_mcangle_it	2.64	5	11927
X-RAY DIFFRACTION	r_scbond_it	5.8	8	4167
X-RAY DIFFRACTION	r_scangle_it	8.133	11	3495
X-RAY DIFFRACTION	r_nbtor_refined	0.189	0.2	5819
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.065	0.2	1

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	904	tight positional	0.05	0.05
1	2	B	904	tight positional	0.05	0.05
1	3	C	904	tight positional	0.04	0.05
1	4	D	904	tight positional	0.05	0.05
1	1	A	1333	loose positional	0.44	5
1	2	B	1333	loose positional	0.47	5
1	3	C	1333	loose positional	0.5	5
1	4	D	1333	loose positional	0.49	5
1	1	A	904	tight thermal	0.15	0.5
1	2	B	904	tight thermal	0.14	0.5
1	3	C	904	tight thermal	0.12	0.5
1	4	D	904	tight thermal	0.14	0.5
1	1	A	1333	loose thermal	2.56	10
1	2	B	1333	loose thermal	2.48	10
1	3	C	1333	loose thermal	2.51	10
1	4	D	1333	loose thermal	2.43	10
2	1	A	113	tight positional	0.04	0.05
2	2	B	113	tight positional	0.04	0.05
2	3	C	113	tight positional	0.05	0.05
2	4	D	113	tight positional	0.04	0.05
2	1	A	130	loose positional	0.22	5
2	2	B	130	loose positional	0.31	5
2	3	C	130	loose positional	0.4	5
2	4	D	130	loose positional	0.23	5
2	1	A	113	tight thermal	0.18	0.5
2	2	B	113	tight thermal	0.11	0.5
2	3	C	113	tight thermal	0.1	0.5
2	4	D	113	tight thermal	0.14	0.5
2	1	A	130	loose thermal	2.15	10
2	2	B	130	loose thermal	2.04	10
2	3	C	130	loose thermal	2.26	10
2	4	D	130	loose thermal	1.48	10
3	1	A	60	tight positional	0.05	0.05
3	2	C	60	tight positional	0.05	0.05
3	3	D	60	tight positional	0.04	0.05
3	1	A	87	loose positional	0.34	5
3	2	C	87	loose positional	0.45	5
3	3	D	87	loose positional	0.31	5
3	1	A	60	tight thermal	0.16	0.5
3	2	C	60	tight thermal	0.13	0.5
3	3	D	60	tight thermal	0.15	0.5
3	1	A	87	loose thermal	2.77	10
3	2	C	87	loose thermal	2.97	10
3	3	D	87	loose thermal	3.85	10
4	1	A	294	tight positional	0.06	0.05
4	2	B	294	tight positional	0.05	0.05
4	3	C	294	tight positional	0.06	0.05
4	1	A	415	loose positional	0.52	5
4	2	B	415	loose positional	0.41	5
4	3	C	415	loose positional	0.54	5
4	1	A	294	tight thermal	0.16	0.5
4	2	B	294	tight thermal	0.12	0.5
4	3	C	294	tight thermal	0.13	0.5
4	1	A	415	loose thermal	3.41	10
4	2	B	415	loose thermal	2.95	10
4	3	C	415	loose thermal	2.69	10
5	1	A	437	tight positional	0.05	0.05
5	2	C	437	tight positional	0.05	0.05
5	3	D	437	tight positional	0.04	0.05
5	1	A	609	loose positional	0.55	5
5	2	C	609	loose positional	0.79	5
5	3	D	609	loose positional	0.56	5
5	1	A	437	tight thermal	0.15	0.5
5	2	C	437	tight thermal	0.12	0.5
5	3	D	437	tight thermal	0.14	0.5
5	1	A	609	loose thermal	3.04	10
5	2	C	609	loose thermal	3.05	10
5	3	D	609	loose thermal	2.51	10
6	1	A	377	tight positional	0.06	0.05
6	2	B	377	tight positional	0.08	0.05
6	3	C	377	tight positional	0.07	0.05
6	4	D	377	tight positional	0.06	0.05
6	1	A	540	loose positional	0.55	5
6	2	B	540	loose positional	0.74	5
6	3	C	540	loose positional	0.57	5
6	4	D	540	loose positional	0.53	5
6	1	A	377	tight thermal	0.16	0.5
6	2	B	377	tight thermal	0.12	0.5
6	3	C	377	tight thermal	0.11	0.5
6	4	D	377	tight thermal	0.15	0.5
6	1	A	540	loose thermal	3.67	10
6	2	B	540	loose thermal	3.74	10
6	3	C	540	loose thermal	3.31	10
6	4	D	540	loose thermal	3.11	10

LS refinement shell

Resolution: 2.61→2.672 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.394	179	4.48 %
R_work	0.326	3819	-
obs	-	-	93.81 %

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	1.8404	-0.1031	0.0568	1.8361	-0.2621	2.5428	-0.1021	0.2848	0.5246	-0.0013	0.1456	0.1757	-0.0907	-0.0432	-0.0435	-0.3054	0.0482	0.0117	-0.2417	0.0702	-0.1234	-16.0468	49.1455	19.0726
2	2.7455	-0.4447	1.285	2.3602	-0.39	2.1614	0.0483	-0.3253	-0.0552	0.2925	0.0077	0.1967	0.0961	-0.2565	-0.056	-0.2198	0.01	0.04	-0.2566	0.0117	-0.4146	-7.745	22.1922	37.0643
3	1.8928	-0.3048	-0.6473	2.976	0.592	1.544	0.0124	0.258	0.1015	-0.2701	-0.0292	0.0921	-0.0884	0.0477	0.0168	-0.2634	0.016	0.0289	-0.2466	0.0373	-0.4021	-8.9332	29.3671	16.406
4	2.3312	-0.3718	-0.1359	1.929	0.0191	1.4061	-0.0398	0.2735	0.5432	-0.2019	0.097	0.3329	-0.1441	-0.0744	-0.0572	-0.2695	0.0326	0.0037	-0.2504	0.1352	0.1039	-17.6861	58.4383	17.9036
5	10.62	2.2405	-4.7069	3.5466	-1.7665	5.2972	0.5079	2.019	0.898	-0.2605	-0.0077	0.4465	-1.0883	-1.4861	-0.5002	0.3279	0.3866	0.0253	0.3262	0.0927	0.2617	-35.9382	82.9941	9.2463
6	7.7671	-1.6566	-0.9066	5.5914	-1.3114	3.5367	0.1633	0.6447	0.5253	-0.5729	-0.2014	-0.7736	-0.366	0.0467	0.0382	0.0716	0.0687	0.1329	-0.1607	0.0421	0.3462	-15.8563	78.3168	11.4574
7	3.1937	0.7021	-0.4831	1.9745	0.2189	1.3947	0.0916	0.42	0.7307	0.0323	0.1877	0.1356	-0.1102	-0.2517	-0.2793	-0.1793	-0.0829	0.0521	-0.0859	0.2925	0.0321	10.2031	60.4584	-4.0488
8	3.6803	1.0731	-1.7671	2.7922	-0.6558	4.2941	0.6492	-1.138	0.7186	0.9507	-0.0018	0.5991	-1.0325	0.6625	-0.6474	0.3969	-0.2875	0.3154	0.1589	-0.0094	0.2408	25.5251	88.8867	4.1883
9	3.4016	0.5015	-1.8266	4.0705	1.4601	3.2505	0.3905	-0.2312	0.6115	0.2487	0.124	0.9519	-0.7383	-0.2269	-0.5145	0.1048	0.0266	0.3234	0.0487	0.3584	0.6493	5.6099	80.1387	1.6806
10	2.4869	0.684	-0.3744	1.7478	0.3355	1.8098	-0.0436	0.4994	0.4559	-0.1554	0.2143	0.0723	-0.0246	-0.338	-0.1707	-0.2237	-0.1139	0.0108	-0.0193	0.245	-0.1597	9.6271	50.7747	-5.6852
11	3.2151	0.4128	1.846	2.1385	0.8756	3.1062	0.0361	0.943	-0.1565	-0.3593	0.1644	-0.2156	0.0839	1.1352	-0.2005	-0.0586	-0.0534	0.061	0.1769	-0.0162	-0.3539	4.6663	22.823	-23.8468
12	2.1524	0.7819	1.5788	3.8751	-0.51	1.6892	-0.028	0.0758	0.1429	0.1393	-0.0374	-0.0183	-0.1354	0.1368	0.0655	-0.2022	-0.0939	0.0418	-0.1168	0.0334	-0.3977	4.9095	30.2439	-3.3242

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	0 - 156	12 - 168
2	2	A	A	157 - 309	169 - 321
3	3	A	A	310 - 376	322 - 388
4	4	B	B	0 - 156	12 - 168
5	5	B	B	157 - 309	169 - 321
6	6	B	B	310 - 376	322 - 388
7	7	C	C	0 - 156	12 - 168
8	8	C	C	157 - 309	169 - 321
9	9	C	C	310 - 376	322 - 388
10	10	D	D	0 - 156	12 - 168
11	11	D	D	157 - 309	169 - 321
12	12	D	D	310 - 376	322 - 388

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Yorodumi