PDB-1vm6: Crystal structure of Dihydrodipicolinate reductase (TM1520) from ...

ID or keywords:

Entry

Database: PDB / ID: 1vm6

Title

Crystal structure of Dihydrodipicolinate reductase (TM1520) from Thermotoga maritima at 2.27 A resolution

Components

Dihydrodipicolinate reductase

4-hydroxy-tetrahydrodipicolinate reductase

Keywords

OXIDOREDUCTASE / TM1520 /

DIHYDRODIPICOLINATE REDUCTASE /

STRUCTURAL GENOMICS / JCSG /

PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics

Function / homology

Function and homology information

4-hydroxy-tetrahydrodipicolinate reductase / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor /

4-hydroxy-tetrahydrodipicolinate reductase / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding /

NADP binding /

cytosol
Similarity search - Function

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.27 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: To be published
Title: Crystal structure of Dihydrodipicolinate reductase (TM1520) from Thermotoga maritima at 2.27 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Sep 3, 2004	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 21, 2004	Provider: repository / Type: Initial release
Revision 1.1	Apr 26, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 4, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.name / _software.version
Revision 1.4	Jan 25, 2023	Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5	Sep 20, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / 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

-
Download

PDBx/mmCIF format	1vm6.cif.gz	196.9 KB	Display	PDBx/mmCIF format
PDB format	pdb1vm6.ent.gz	156.6 KB	Display	PDB format
PDBx/mmJSON format	1vm6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vm/1vm6 ftp://data.pdbj.org/pub/pdb/validation_reports/vm/1vm6	HTTPS FTP

-
Related structure data

Related structure data	1arzS S: Starting model for refinement
Similar structure data	5tej-d 5ten-1 5us6-1 5us6-2 1arz-d 5us6-3 6l1q-d 3ijp-1 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: 283377

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Dihydrodipicolinate reductase

B: Dihydrodipicolinate reductase

C: Dihydrodipicolinate reductase

D: Dihydrodipicolinate reductase

hetero molecules

105 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)	133.077, 109.217, 112.602
Angle α, β, γ (deg.)	90.00, 119.23, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
1	2	A
2	2	B
3	2	C
4	2	D
1	3	A
2	3	B
3	3	C
4	3	D

NCS domain segments:

Component-ID: 1 / Refine code: 2

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	MET	MET	PHE	PHE	A	A	1 - 98	13 - 110
2	1	MET	MET	PHE	PHE	B	B	1 - 98	13 - 110
3	1	MET	MET	PHE	PHE	C	C	1 - 98	13 - 110
4	1	MET	MET	PHE	PHE	D	D	1 - 98	13 - 110
1	2	SER	SER	ILE	ILE	A	A	99 - 182	111 - 194
2	2	SER	SER	ILE	ILE	B	B	99 - 182	111 - 194
3	2	SER	SER	ILE	ILE	C	C	99 - 182	111 - 194
4	2	SER	SER	ILE	ILE	D	D	99 - 182	111 - 194
1	3	SER	SER	ILE	ILE	A	A	183 - 212	195 - 224
2	3	SER	SER	ILE	ILE	B	B	183 - 212	195 - 224
3	3	SER	SER	ILE	ILE	C	C	183 - 212	195 - 224
4	3	SER	SER	ILE	ILE	D	D	183 - 212	195 - 224

NCS ensembles :

ID
1
2
3

-
Protein , 1 types, 4 molecules ABCD

#1: Protein	Dihydrodipicolinate reductase / 4-hydroxy-tetrahydrodipicolinate reductase / DHPR Mass: 25225.061 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: dapB, TM1520 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1K8, EC: 1.3.1.26

-
Non-polymers , 5 types, 550 molecules

#2: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#4: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 3.38 Å³/Da / Density % sol: 63.36 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.5 Details: 20.0% PEG-400, 0.2M Ca(OAc)2, 0.1M Acetate pH 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.980075
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 24, 2004 / Details: flat mirror
Radiation	Monochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.980075 Å / Relative weight: 1
Reflection	Resolution: 2.27→29.03 Å / Num. obs: 61963 / % possible obs: 47.8 % / Redundancy: 3.6 % / B_iso Wilson estimate: 46.59 Å² / R_sym value: 0.086 / Net I/σ(I): 10.8
Reflection shell	Resolution: 2.27→2.39 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2 / Num. unique all: 7228 / R_sym value: 0.507 / % possible all: 38.4

-
Processing

Software

Name	Version	Classification
XDS		data scaling
XSCALE		data scaling
SCALA	4.2)	data scaling
MOLREP		phasing
REFMAC	5.2.0005	refinement
XDS		data reduction
CCP4	(SCALA)	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1arz

1arz

Resolution: 2.27→29.03 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.943 / SU B: 10.618 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21256	3151	5.1 %	RANDOM
R_work	0.17127	-	-	-
obs	0.17334	58811	95.49 %	-

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: 42.509 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.77 Å²	0 Å²	-0.6 Å²
2-	-	0.29 Å²	0 Å²
3-	-	-	-2.64 Å²

Refinement step

Cycle: LAST / Resolution: 2.27→29.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6730	0	275	529	7534

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	7142
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	6640
X-RAY DIFFRACTION	r_angle_refined_deg	1.596	2.008	9642
X-RAY DIFFRACTION	r_angle_other_deg	0.919	3	15462
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.804	5	861
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.816	24.216	287
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.438	15	1241
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.957	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	1095
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	7671
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1333
X-RAY DIFFRACTION	r_nbd_refined	0.196	0.2	1370
X-RAY DIFFRACTION	r_nbd_other	0.177	0.2	6699
X-RAY DIFFRACTION	r_nbtor_other	0.086	0.2	4282
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.175	0.2	436
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.196	0.2	20
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.205	0.2	63
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.187	0.2	21
X-RAY DIFFRACTION	r_mcbond_it	1.237	3	4646
X-RAY DIFFRACTION	r_mcbond_other	0.526	3	1785
X-RAY DIFFRACTION	r_mcangle_it	1.742	5	6938
X-RAY DIFFRACTION	r_scbond_it	3.936	8	3071
X-RAY DIFFRACTION	r_scangle_it	5.093	11	2704
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	3359

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	575	tight positional	0.05	0.05
1	2	B	575	tight positional	0.07	0.05
1	3	C	575	tight positional	0.05	0.05
1	4	D	575	tight positional	0.04	0.05
1	1	A	915	medium positional	0.59	0.5
1	2	B	915	medium positional	0.87	0.5
1	3	C	915	medium positional	0.61	0.5
1	4	D	915	medium positional	0.56	0.5
1	1	A	575	tight thermal	0.09	0.5
1	2	B	575	tight thermal	0.15	0.5
1	3	C	575	tight thermal	0.1	0.5
1	4	D	575	tight thermal	0.1	0.5
1	1	A	915	medium thermal	0.6	2
1	2	B	915	medium thermal	0.91	2
1	3	C	915	medium thermal	0.73	2
1	4	D	915	medium thermal	0.72	2
2	1	A	493	tight positional	0.06	0.05
2	2	B	493	tight positional	0.09	0.05
2	3	C	493	tight positional	0.09	0.05
2	4	D	493	tight positional	0.09	0.05
2	1	A	788	medium positional	0.71	0.5
2	2	B	788	medium positional	0.9	0.5
2	3	C	788	medium positional	0.85	0.5
2	4	D	788	medium positional	0.77	0.5
2	1	A	493	tight thermal	0.13	0.5
2	2	B	493	tight thermal	0.15	0.5
2	3	C	493	tight thermal	0.14	0.5
2	4	D	493	tight thermal	0.16	0.5
2	1	A	788	medium thermal	0.82	2
2	2	B	788	medium thermal	0.95	2
2	3	C	788	medium thermal	1	2
2	4	D	788	medium thermal	0.89	2
3	1	A	176	tight positional	0.08	0.05
3	2	B	176	tight positional	0.09	0.05
3	3	C	176	tight positional	0.1	0.05
3	4	D	176	tight positional	0.06	0.05
3	1	A	272	medium positional	0.64	0.5
3	2	B	272	medium positional	0.65	0.5
3	3	C	272	medium positional	0.89	0.5
3	4	D	272	medium positional	0.63	0.5
3	1	A	176	tight thermal	0.11	0.5
3	2	B	176	tight thermal	0.12	0.5
3	3	C	176	tight thermal	0.16	0.5
3	4	D	176	tight thermal	0.11	0.5
3	1	A	272	medium thermal	0.89	2
3	2	B	272	medium thermal	0.92	2
3	3	C	272	medium thermal	1.03	2
3	4	D	272	medium thermal	0.71	2

LS refinement shell

Resolution: 2.27→2.329 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.32	185	5.43 %
R_work	0.261	3220	-
obs	-	-	71.93 %

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	3.9168	0.0448	-0.4041	4.6471	-0.0355	3.7069	-0.0202	0.0513	0.5971	0.4511	0.2434	0.3464	-0.7693	-0.6104	-0.2232	0.1409	0.226	0.1105	-0.0257	0.1842	-0.0214	12.9957	34.1037	23.6416
2	2.7191	-0.479	-0.4304	3.3681	1.1335	3.4248	-0.1642	-0.1852	0.1478	0.0974	0.1069	0.0281	-0.3812	-0.0745	0.0573	-0.3245	0.062	-0.0113	-0.2798	0.0059	-0.2088	24.1122	12.7793	59.9664
3	5.0873	2.2945	-0.4862	5.7868	-0.7988	5.8735	-0.4359	0.5899	-0.6593	-0.9594	0.5106	-0.4325	1.1435	-0.105	-0.0748	0.1902	-0.32	0.0988	-0.0555	-0.1711	-0.0178	15.1416	-36.2354	20.7533
4	2.7967	-1.2484	-0.7013	4.0903	1.7099	6.5955	0.027	0.0815	-0.2094	-0.0866	0.168	-0.3586	0.5801	0.7964	-0.195	-0.1217	-0.0502	0.0369	-0.0645	-0.1316	-0.1046	50.0445	-17.1882	9.6694
5	0.9774	-0.2524	-0.0655	4.0484	-0.1904	0.526	-0.0049	0.2864	0.0785	-0.1964	0.1704	-0.1465	-0.3275	-0.3134	-0.1655	-0.1522	-0.0056	-0.0474	-0.0655	0.0963	-0.1874	21.3229	14.6377	18.2619
6	0.8702	-0.2977	-0.5961	1.2176	1.3758	3.5062	-0.1455	0.0709	-0.113	0.1046	0.0405	0.1744	0.091	-0.3256	0.1049	-0.3425	-0.0175	-0.0155	-0.2418	0.0462	-0.1818	23.202	-1.1098	43.2625
7	0.33	0.2303	0.0292	3.2387	-0.4903	0.9069	-0.1523	0.2138	-0.1314	-0.132	0.1831	0.2702	0.0909	-0.3745	-0.0308	-0.2659	-0.1488	-0.0348	-0.0282	-0.0064	-0.1012	13.1507	-12.019	27.3297
8	1.1828	-1.234	-0.9269	2.388	1.4382	3.112	-0.0165	0.2508	-0.0199	-0.4265	0.1102	-0.1657	-0.3275	-0.0058	-0.0937	-0.2478	-0.143	-0.0256	-0.1738	-0.0255	-0.1992	38.5577	-0.8993	18.3246

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 - 99	13 - 111
2	2	B	B	1 - 99	13 - 111
3	3	C	C	1 - 99	13 - 111
4	4	D	D	1 - 99	13 - 111
5	5	A	A	101 - 212	113 - 224
6	6	B	B	101 - 212	113 - 224
7	7	C	C	101 - 212	113 - 224
8	8	D	D	101 - 212	113 - 224

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and 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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 550 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
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

-Protein , 1 types, 4 molecules ABCD

-Non-polymers , 5 types, 550 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 550 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
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