PDB-4kde: Crystal Structure of the Apo Form of Thermus thermophilus Malate ...

ID or keywords:

Entry

Database: PDB / ID: 4kde

Title

Crystal Structure of the Apo Form of Thermus thermophilus Malate Dehydrogenase

Components

Malate dehydrogenase

Keywords

OXIDOREDUCTASE / Dehydrogenase

Function / homology

Function and homology information

malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / oxaloacetate metabolic process / NADH metabolic process / tricarboxylic acid cycle
Similarity search - Function

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.798 Å

Authors

Hsu, C.-H. / Hong, C.-H. / Chang, Y.-Y.

Citation

Journal: Plos One / Year: 2013
Title: Crystal structures and molecular dynamics simulations of thermophilic malate dehydrogenase reveal critical loop motion for co-substrate binding.
Authors: Hung, C.H. / Hwang, T.S. / Chang, Y.Y. / Luo, H.R. / Wu, S.P. / Hsu, C.H.

History

Deposition	Apr 25, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 5, 2014	Provider: repository / Type: Initial release
Revision 1.1	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4kde.cif.gz	273.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4kde.ent.gz	222.1 KB	Display	PDB format
PDBx/mmJSON format	4kde.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4kde_validation.pdf.gz	431.6 KB	Display	wwPDB validaton report
Full document	4kde_full_validation.pdf.gz	435.3 KB	Display
Data in XML	4kde_validation.xml.gz	32.3 KB	Display
Data in CIF	4kde_validation.cif.gz	50.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kd/4kde ftp://data.pdbj.org/pub/pdb/validation_reports/kd/4kde	HTTPS FTP

-
Related structure data

Related structure data	4kdfC C: citing same article (ref.)
Similar structure data	2zeu-d 1iz9-d 1civ-1 1wze-d 4uum-d 3d5t-1 2e8w-d 4uul-d 1smr-7 7mdh-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (10) #102 - Jun 2008 Lactate Dehydrogenase similarity (6) #142 - Oct 2011 PDB Pioneers similarity (6)

Deposited unit

A: Malate dehydrogenase

B: Malate dehydrogenase

74.3 kDa, 2 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)	71.173, 86.006, 118.117
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Malate dehydrogenase Mass: 37150.695 Da / Num. of mol.: 2 / Fragment: Malate Dehydrogenase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: mdh / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(ED3) / References: UniProt: P10584, malate dehydrogenase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 846 / 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: 2.43 Å³/Da / Density % sol: 49.44 %
Crystal grow	Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 22.5% PEG 4000, 1.0M Tris-HCl, 0.2M MgCl2, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 283K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 6, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.798→30 Å / Num. all: 68067 / Num. obs: 67995 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / R_merge(I) obs: 0.061 / R_sym value: 0.061 / Net I/σ(I): 27.713
Reflection shell	Resolution: 1.798→1.86 Å / Redundancy: 6 % / R_merge(I) obs: 0.301 / Mean I/σ(I) obs: 6.11 / Num. unique all: 6688 / R_sym value: 0.301 / % possible all: 99.5

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.798→27.86 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 15.51 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1698	2000	2.94 %	RANDOM
R_work	0.144	-	-	-
all	0.1448	68067	-	-
obs	0.1448	67995	99.88 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.798→27.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5029	0	0	846	5875

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5117
X-RAY DIFFRACTION	f_angle_d	1.05	6925
X-RAY DIFFRACTION	f_dihedral_angle_d	13.127	1913
X-RAY DIFFRACTION	f_chiral_restr	0.071	783
X-RAY DIFFRACTION	f_plane_restr	0.005	907

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.798-1.843	0.1862	139	0.1681	4611	X-RAY DIFFRACTION	99
1.843-1.8928	0.2264	142	0.1584	4658	X-RAY DIFFRACTION	100
1.8928-1.9485	0.2147	141	0.1484	4663	X-RAY DIFFRACTION	100
1.9485-2.0113	0.1771	141	0.149	4656	X-RAY DIFFRACTION	100
2.0113-2.0832	0.1895	142	0.1454	4692	X-RAY DIFFRACTION	100
2.0832-2.1666	0.1754	142	0.138	4669	X-RAY DIFFRACTION	100
2.1666-2.2652	0.1746	142	0.1422	4683	X-RAY DIFFRACTION	100
2.2652-2.3845	0.1754	142	0.1426	4693	X-RAY DIFFRACTION	100
2.3845-2.5338	0.1787	143	0.1446	4712	X-RAY DIFFRACTION	100
2.5338-2.7293	0.1699	142	0.1464	4703	X-RAY DIFFRACTION	100
2.7293-3.0037	0.1747	144	0.1473	4736	X-RAY DIFFRACTION	100
3.0037-3.4376	0.1341	144	0.143	4762	X-RAY DIFFRACTION	100
3.4376-4.3284	0.1508	146	0.1268	4785	X-RAY DIFFRACTION	100
4.3284-27.8631	0.1686	150	0.151	4972	X-RAY DIFFRACTION	99

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	1.9847	0.169	0.2855	1.3894	0.2521	1.0635	0.0236	-0.0058	0.1757	0.0047	-0.023	0.0296	-0.0466	-0.0307	-0.0109	0.0741	0.0037	0.0057	0.0454	-0.0014	0.0722	-2.4892	35.126	14.8794
2	3.3624	0.5506	-0.4451	2.0748	0.1686	2.4875	0.0438	-0.5206	-0.1026	0.5154	0.0022	0.4365	-0.0311	-0.3358	0.0307	0.1661	0.0164	0.0405	0.2018	-0.014	0.1987	-21.58	27.9275	20.7414
3	0.9392	-0.4334	0.0568	1.8918	0.0247	0.776	0.0403	0.0885	-0.0516	-0.0936	-0.0542	0.0307	0.0738	-0.0219	0.0317	0.0803	-0.0025	-0.0051	0.09	-0.012	0.0527	-9.1923	13.6314	8.7643
4	0.6423	0.2701	0.2073	1.2268	-0.2064	1.1236	0.0511	-0.0279	-0.0918	0.0446	-0.0392	-0.0105	0.1492	0.0453	-0.0134	0.0686	0.0159	0.0022	0.0577	-0.002	0.0778	-4.4998	8.5202	16.0501
5	1.8367	0.1981	0.3421	1.7838	0.1225	1.1781	-0.0467	0.176	0.0359	-0.2741	0.0536	0.0458	0.0735	-0.007	0.0041	0.1198	0.0038	-0.0148	0.0695	-0.0042	0.0523	-12.665	12.6964	0.3048
6	2.3903	-1.7059	-0.143	3.727	0.1815	1.2113	-0.0294	-0.0937	-0.0891	0.122	-0.0203	0.506	0.0522	-0.1784	-0.0211	0.106	-0.0427	-0.0158	0.1646	0.0005	0.1553	-26.0589	11.8785	11.2311
7	2.0753	0.4244	0.2633	1.7327	0.1897	1.4943	0.0466	-0.0525	-0.0633	0.046	0.0258	-0.0761	0.1622	0.122	-0.0429	0.0861	0.0316	-0.0152	0.0666	-0.0046	0.0738	13.2447	14.8739	22.8585
8	5.2214	0.4652	-0.8762	4.0339	1.5198	6.606	-0.1032	-0.812	0.165	1.2288	0.2075	0.1737	-0.0538	0.0242	-0.0328	0.3967	0.0813	-0.0409	0.2791	0.0031	0.1601	20.2822	22.0139	41.5614
9	3.1812	-0.6262	1.2634	3.0963	-0.358	2.4223	-0.0574	-0.1924	-0.025	0.2596	0.1325	-0.4635	0.0867	0.408	0.0015	0.1013	0.0191	-0.0414	0.2071	-0.0267	0.1651	27.6994	24.213	29.9644
10	4.7381	-1.0154	0.4986	4.4085	-1.2505	1.5097	0.0163	0.1472	0.0883	-0.2074	0.1387	0.1201	-0.2126	0.1403	-0.1089	0.1059	-0.0428	0.0326	0.0921	-0.0423	0.0747	15.8424	43.6891	18.739
11	1.1792	-0.0033	-0.2112	1.1225	0.6223	0.7725	0.0343	-0.0508	0.1493	-0.0797	0.0586	-0.1254	-0.1405	0.1603	-0.0709	0.1117	-0.0308	0.0144	0.1093	-0.024	0.0947	17.4011	41.956	23.4039
12	2.253	1.8896	0.7562	2.5999	1.1009	1.9966	0.1125	-0.0576	-0.0573	-0.0642	0.2605	-0.5319	-0.0616	0.4608	-0.2287	0.074	-0.0198	0.0067	0.2362	-0.0934	0.2454	32.7518	37.7025	23.844
13	1.9397	-1.0685	0.7849	5.3995	-2.3344	2.8745	0.0168	-0.3563	-0.0441	0.6985	0.1537	-0.5378	-0.0578	0.3253	-0.1244	0.2245	-0.0107	-0.0923	0.3648	-0.1293	0.2645	30.0344	38.3849	39.2956

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 86 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 87 through 119 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 120 through 204 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 205 through 254 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 255 through 300 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 301 through 331 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 86 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 87 through 119 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 120 through 156 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 157 through 184 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 185 through 267 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 268 through 300 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 301 through 329 )

-
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

-
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

-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

-
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