PDB-4kt2: Crystal structure of d-mannonate dehydratase from chromohalobacte...

ID or keywords:

Entry

Database: PDB / ID: 4kt2

Title

Crystal structure of d-mannonate dehydratase from chromohalobacter salexigens complexed with mg and glycerol

Components

D-mannonate dehydratase

Keywords

HYDROLASE / Enolase fold / D-MANNONATE DEHYDRATASE

Function / homology

Function and homology information

gluconate dehydratase /

gluconate dehydratase activity /

mannonate dehydratase /

mannonate dehydratase activity /

Lyases; Carbon-oxygen lyases; Hydro-lyases / amino acid catabolic process / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function

Biological species

Chromohalobacter salexigens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.798 Å

Authors

Fedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C.

Citation

Journal: To be Published
Title: Crystal structure of d-mannonate dehydratase from chromohalobacter salexigens complexed with mg and glycerol
Authors: Fedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C.

History

Deposition	May 19, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 21, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 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_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4kt2.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb4kt2.ent.gz	1017.6 KB	Display	PDB format
PDBx/mmJSON format	4kt2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kt/4kt2 ftp://data.pdbj.org/pub/pdb/validation_reports/kt/4kt2	HTTPS FTP

-
Related structure data

Related structure data	3ow1S 4kpl S: Starting model for refinement
Similar structure data	3p93-4 3rgt-2 4kpl-3 4kws-1 4k2s-3 3ow1-1 3p93-3 4kws-3 4kpl-1 4kpl-4 3ow1-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

3ow1S

4kpl

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (2)

Deposited unit

A: D-mannonate dehydratase

B: D-mannonate dehydratase

C: D-mannonate dehydratase

D: D-mannonate dehydratase

E: D-mannonate dehydratase

F: D-mannonate dehydratase

G: D-mannonate dehydratase

H: D-mannonate dehydratase

hetero molecules

366 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: D-mannonate dehydratase

E: D-mannonate dehydratase

hetero molecules

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

2

B: D-mannonate dehydratase

D: D-mannonate dehydratase

hetero molecules

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

3

C: D-mannonate dehydratase

G: D-mannonate dehydratase

hetero molecules

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

4

F: D-mannonate dehydratase

H: D-mannonate dehydratase

hetero molecules

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

Unit cell

Length a, b, c (Å)	86.585, 177.787, 109.993
Angle α, β, γ (deg.)	90.00, 102.62, 90.00
Int Tables number	4
Space group name H-M	P12₁1

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein	D-mannonate dehydratase Mass: 45468.258 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromohalobacter salexigens (bacteria) / Strain: DSM 3043 / ATCC BAA-138 / NCIMB 13768 / Gene: Csal_2974 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1QT89, mannonate dehydratase

-
Non-polymers , 5 types, 2244 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 2209 / 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: 2.27 Å³/Da / Density % sol: 45.84 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.5M ammonium sulfate, 0.1M bis-tris, 0.1M sodium chloride , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2010
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.798→35.172 Å / Num. all: 295190 / Num. obs: 295190 / % possible obs: 98.48 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software

Name	Version	Classification
CBASS		data collection
BALBES		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3OW1

3ow1

Resolution: 1.798→35.172 Å / SU ML: 0.41 / σ(F): 0 / Phase error: 17.9 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.182	14932	5.06 %	RANDOM
R_work	0.149	-	-	-
all	0.1507	295190	-	-
obs	0.1507	295190	98.48 %	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 41.238 Å² / k_sol: 0.4 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.819 Å²	0 Å²	2.7657 Å²
2-	-	-1.2552 Å²	-0 Å²
3-	-	-	-2.5638 Å²

Refinement step

Cycle: LAST / Resolution: 1.798→35.172 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24554	0	136	2209	26899

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	25439
X-RAY DIFFRACTION	f_angle_d	1.041	34665
X-RAY DIFFRACTION	f_dihedral_angle_d	12.724	9118
X-RAY DIFFRACTION	f_chiral_restr	0.073	3728
X-RAY DIFFRACTION	f_plane_restr	0.005	4506

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 (%)
1.7982-1.8186	0.3143	353	0.2594	7204	X-RAY DIFFRACTION	76
1.8186-1.84	0.2752	497	0.2388	8510	X-RAY DIFFRACTION	90
1.84-1.8625	0.2607	475	0.2299	9115	X-RAY DIFFRACTION	96
1.8625-1.886	0.2385	522	0.2029	9456	X-RAY DIFFRACTION	100
1.886-1.9109	0.2461	499	0.1982	9403	X-RAY DIFFRACTION	100
1.9109-1.937	0.2438	507	0.188	9478	X-RAY DIFFRACTION	100
1.937-1.9647	0.2198	527	0.1751	9426	X-RAY DIFFRACTION	100
1.9647-1.994	0.2361	501	0.1741	9418	X-RAY DIFFRACTION	100
1.994-2.0252	0.2061	527	0.1639	9437	X-RAY DIFFRACTION	100
2.0252-2.0584	0.1941	545	0.1583	9428	X-RAY DIFFRACTION	100
2.0584-2.0939	0.1977	539	0.1521	9393	X-RAY DIFFRACTION	100
2.0939-2.1319	0.2118	492	0.1537	9447	X-RAY DIFFRACTION	100
2.1319-2.1729	0.1831	504	0.1488	9473	X-RAY DIFFRACTION	100
2.1729-2.2173	0.1882	461	0.1445	9505	X-RAY DIFFRACTION	100
2.2173-2.2655	0.1785	508	0.1421	9415	X-RAY DIFFRACTION	100
2.2655-2.3182	0.1863	497	0.1446	9449	X-RAY DIFFRACTION	100
2.3182-2.3761	0.1893	525	0.1456	9454	X-RAY DIFFRACTION	100
2.3761-2.4404	0.1849	492	0.1446	9503	X-RAY DIFFRACTION	100
2.4404-2.5122	0.1889	516	0.1394	9426	X-RAY DIFFRACTION	100
2.5122-2.5932	0.1882	470	0.1436	9476	X-RAY DIFFRACTION	100
2.5932-2.6859	0.202	470	0.146	9494	X-RAY DIFFRACTION	100
2.6859-2.7934	0.1795	513	0.1485	9439	X-RAY DIFFRACTION	100
2.7934-2.9204	0.1878	512	0.1503	9451	X-RAY DIFFRACTION	100
2.9204-3.0743	0.1789	497	0.1471	9485	X-RAY DIFFRACTION	100
3.0743-3.2668	0.1758	488	0.1437	9462	X-RAY DIFFRACTION	100
3.2668-3.5188	0.1577	497	0.1341	9483	X-RAY DIFFRACTION	100
3.5188-3.8726	0.1511	475	0.1251	9532	X-RAY DIFFRACTION	100
3.8726-4.432	0.1373	474	0.1188	9499	X-RAY DIFFRACTION	100
4.432-5.5802	0.1559	543	0.1337	9435	X-RAY DIFFRACTION	99
5.5802-35.1786	0.1647	506	0.1693	9562	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	0.2472	-0.0521	-0.0298	0.3813	-0.0176	0.2911	0.0115	-0.0038	0.0584	-0.0168	0.0268	-0.1348	-0.0513	0.0827	-0.0306	0.0666	-0.0198	0.0034	0.1125	-0.0135	0.1347	30.221	9.184	25.8408
2	0.2176	-0.066	-0.0056	0.6134	0.0097	0.5063	-0.0285	-0.0385	-0.03	0.1506	-0.0022	0.1078	0.1129	-0.0824	0.0204	0.1544	-0.0213	0.0404	0.11	-0.0055	0.1193	-10.8075	-35.6595	51.0702
3	0.4012	-0.0119	-0.228	0.4096	0.1325	0.4953	-0.016	-0.1034	-0.0037	0.1615	0.0215	-0.0697	0.0639	0.1163	-0.0013	0.1672	0.0165	-0.0401	0.1368	-0.0093	0.0997	18.3542	-12.2559	63.0824
4	0.3936	0.0886	-0.0419	0.5522	0.0979	0.3819	-0.0166	-0.0337	-0.0835	0.1583	0.0199	-0.081	0.145	0.078	-0.0021	0.1787	0.0411	-0.0167	0.1111	0.0113	0.1238	17.2071	-50.9783	40.5923
5	0.3237	0.0404	-0.168	0.5795	0.0276	0.4307	0.022	0.086	0.0362	-0.1302	-0.0193	0.0414	-0.0725	-0.0674	-0.0047	0.1319	0.0185	-0.0179	0.1418	0.0096	0.1128	5.9697	2.3237	3.3371
6	0.3258	-0.1308	-0.0604	0.6575	0.1136	0.3807	-0.0125	0.0569	-0.0416	-0.0489	-0.0122	0.0671	0.0357	-0.0475	0.0239	0.0881	-0.0127	-0.0059	0.128	-0.0212	0.0999	-1.6676	-41.6137	7.7917
7	0.2507	0.1299	0.0549	0.6674	0.1806	0.4677	0.0032	-0.0147	0.0537	0.0635	-0.0167	0.0837	-0.0126	-0.0228	0.0149	0.0928	0.0048	0.01	0.1021	-0.0106	0.1191	-2.59	8.1083	46.6464
8	0.2311	0.003	0.0503	0.5468	0.0599	0.5503	-0.0083	0.0453	-0.0096	-0.09	0.0061	-0.1271	0.0188	0.0842	0.0054	0.0874	0.0057	0.0229	0.1347	-0.0158	0.1289	29.3058	-29.5241	3.3579

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A
2	X-RAY DIFFRACTION	2	chain B
3	X-RAY DIFFRACTION	3	chain C
4	X-RAY DIFFRACTION	4	chain D
5	X-RAY DIFFRACTION	5	chain E
6	X-RAY DIFFRACTION	6	chain F
7	X-RAY DIFFRACTION	7	chain G
8	X-RAY DIFFRACTION	8	chain H

-
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, 8 molecules ABCDEFGH

-
Non-polymers , 5 types, 2244 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, 8 molecules ABCDEFGH

-Non-polymers , 5 types, 2244 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, 8 molecules ABCDEFGH

-
Non-polymers , 5 types, 2244 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