PDB-8u99: Crystal Structure of Cystathionine beta lyase from Klebsiella aer...

ID or keywords:

Entry

Database: PDB / ID: 8u99

Title

Crystal Structure of Cystathionine beta lyase from Klebsiella aerogenes (PLP-Serine adduct)

Components

Cystathionine beta-lyase

Keywords

LIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE

Function / homology

Function and homology information

L-cysteine catabolic process to pyruvate / cysteine-S-conjugate beta-lyase activity / cysteine-S-conjugate beta-lyase / transsulfuration / methionine biosynthetic process / pyridoxal phosphate binding / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Klebsiella aerogenes KCTC 2190 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal Structure of Cystathionine beta lyase from Klebsiella aerogenes (PLP-Serine adduct)
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Cooper, A.

History

Deposition	Sep 18, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 27, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8u99.cif.gz	326.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8u99.ent.gz	263.9 KB	Display	PDB format
PDBx/mmJSON format	8u99.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8u99_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	8u99_full_validation.pdf.gz	1.6 MB	Display
Data in XML	8u99_validation.xml.gz	34.6 KB	Display
Data in CIF	8u99_validation.cif.gz	51.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u9/8u99 ftp://data.pdbj.org/pub/pdb/validation_reports/u9/8u99	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Cystathionine beta-lyase

B: Cystathionine beta-lyase

hetero molecules

89.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	87.814, 131.172, 82.672
Angle α, β, γ (deg.)	90.00, 103.93, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-654- HOH
2	1	A-684- HOH
3	1	B-588- HOH
4	1	B-666- HOH
5	1	B-670- HOH

-
Protein , 1 types, 2 molecules AB

#1: Protein	Cystathionine beta-lyase Mass: 44102.242 Da / Num. of mol.: 2 / Mutation: V244I, L360P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes KCTC 2190 (bacteria) Gene: EAE_03480 / Plasmid: KlaeA.00906.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3FMF8, cystathionine beta-lyase

#1: Protein

Cystathionine beta-lyase

Mass: 44102.242 Da / Num. of mol.: 2 / Mutation: V244I, L360P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Klebsiella aerogenes KCTC 2190 (bacteria)
Gene: EAE_03480 / Plasmid: KlaeA.00906.a.B1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3FMF8, cystathionine beta-lyase

-
Non-polymers , 5 types, 592 molecules

#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SER / SERINE Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₇NO₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 583 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.62 Å³/Da / Density % sol: 53.05 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Morpheus B12: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Tris/BICINE, pH 8.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI, 2mM PLP and serine added to the protein prior to ...Details: Morpheus B12: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Tris/BICINE, pH 8.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI, 2mM PLP and serine added to the protein prior to crystallization, KlaeA.00906.a.B1.PW39169 at 41.1 mg/mL. Plate 13534 well B12 drop 3, Puck: PSL-0907, Cryo: Direct

Crystal

Density Matthews: 2.62 Å³/Da / Density % sol: 53.05 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus B12: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Tris/BICINE, pH 8.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI, 2mM PLP and serine added to the protein prior to ...

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 6, 2023
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.8→80.24 Å / Num. obs: 81645 / % possible obs: 97.5 % / Redundancy: 4.5 % / CC_1/2: 0.993 / R_merge(I) obs: 0.138 / R_pim(I) all: 0.073 / R_rim(I) all: 0.157 / Χ²: 1.03 / Net I/σ(I): 6.9 / Num. measured all: 367351
Reflection shell	Resolution: 1.8→1.85 Å / % possible obs: 96.4 % / Redundancy: 4.4 % / R_merge(I) obs: 1.001 / Num. measured all: 26257 / Num. unique obs: 5901 / CC_1/2: 0.557 / R_pim(I) all: 0.533 / R_rim(I) all: 1.138 / Χ²: 1.01 / Net I/σ(I) obs: 1.6

-
Processing

Software

Name	Version	Classification
PHENIX	(1.21rc1_5057: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→42.06 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2074	4044	4.96 %
R_work	0.1656	-	-
obs	0.1677	81612	97.39 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.8→42.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5991	0	63	583	6637

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	6345
X-RAY DIFFRACTION	f_angle_d	0.991	8636
X-RAY DIFFRACTION	f_dihedral_angle_d	13.688	2270
X-RAY DIFFRACTION	f_chiral_restr	0.055	970
X-RAY DIFFRACTION	f_plane_restr	0.01	1124

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 (%)
1.8-1.82	0.3326	143	0.2791	2576	X-RAY DIFFRACTION	97
1.82-1.84	0.317	134	0.2784	2677	X-RAY DIFFRACTION	96
1.84-1.87	0.3211	131	0.2722	2635	X-RAY DIFFRACTION	96
1.87-1.89	0.2884	145	0.2585	2612	X-RAY DIFFRACTION	96
1.89-1.92	0.2801	142	0.2378	2618	X-RAY DIFFRACTION	97
1.92-1.94	0.3012	136	0.2286	2631	X-RAY DIFFRACTION	96
1.94-1.97	0.2638	143	0.2246	2701	X-RAY DIFFRACTION	97
1.97-2	0.2536	120	0.211	2621	X-RAY DIFFRACTION	97
2-2.04	0.2426	120	0.2086	2671	X-RAY DIFFRACTION	97
2.04-2.07	0.2547	153	0.2049	2654	X-RAY DIFFRACTION	97
2.07-2.11	0.2569	152	0.2022	2630	X-RAY DIFFRACTION	97
2.11-2.15	0.2168	143	0.1993	2658	X-RAY DIFFRACTION	98
2.15-2.19	0.2615	166	0.1857	2678	X-RAY DIFFRACTION	97
2.19-2.24	0.2235	149	0.1801	2657	X-RAY DIFFRACTION	97
2.24-2.29	0.2201	125	0.1727	2681	X-RAY DIFFRACTION	97
2.29-2.35	0.2112	126	0.1695	2675	X-RAY DIFFRACTION	98
2.35-2.42	0.2189	147	0.157	2687	X-RAY DIFFRACTION	98
2.42-2.49	0.1924	125	0.158	2700	X-RAY DIFFRACTION	98
2.49-2.57	0.2033	156	0.1546	2644	X-RAY DIFFRACTION	98
2.57-2.66	0.1964	150	0.156	2696	X-RAY DIFFRACTION	98
2.66-2.76	0.2054	124	0.1568	2689	X-RAY DIFFRACTION	98
2.76-2.89	0.2208	139	0.1557	2716	X-RAY DIFFRACTION	98
2.89-3.04	0.2122	148	0.1569	2718	X-RAY DIFFRACTION	98
3.04-3.23	0.2103	123	0.1524	2692	X-RAY DIFFRACTION	98
3.23-3.48	0.1945	131	0.151	2697	X-RAY DIFFRACTION	98
3.48-3.83	0.1608	131	0.1374	2715	X-RAY DIFFRACTION	98
3.83-4.39	0.1636	158	0.1235	2727	X-RAY DIFFRACTION	99
4.39-5.53	0.1351	150	0.1215	2747	X-RAY DIFFRACTION	99
5.53-42.06	0.1992	134	0.1573	2765	X-RAY DIFFRACTION	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	0.032	0.002	0.0177	0.0049	0.0022	0.0095	0.0974	-0.0293	-0.013	-0.0043	-0.0459	0.0487	0.0484	-0.0924	-0	0.1262	-0.0061	0.0182	0.1317	0.0066	0.1223	27.8926	-9.4606	-4.5835
2	0.1369	0.023	0.1011	0.006	0.0168	0.0759	-0.0233	-0.1766	0.1315	0.0454	-0.0147	0.0117	-0.0766	-0.0989	-0.0755	0.1463	0.0298	0.0366	0.1227	-0.031	0.1427	34.8557	8.6739	12.0197
3	0.0045	-0.0003	-0.015	0.0013	-0.0023	0.017	-0.0109	-0.2269	-0.0213	0.0165	0.0239	-0.006	0.03	-0.0227	0.0344	0.1363	-0.0593	0.0618	0.3177	-0.0099	0.0396	35.4276	-6.2107	27.3377
4	0.0702	-0.0399	0.0238	0.0244	-0.0105	0.0094	-0.0282	-0.2006	0.0264	0.0031	0.0179	-0.0658	-0.001	0	-0.0105	0.1404	-0.0378	0.0262	0.2313	-0.0158	0.0969	50.5041	-3.5987	30.0946
5	2	5.0569	-4.8214	2	-4.6978	2	-0.4761	-0.298	-1.103	0.3687	-0.2977	0.1264	1.075	-1.3711	0.7741	0.1398	0.0343	0.0111	0.1549	0.0004	0.1934	46.9401	-1.2443	17.3588
6	0.1169	-0.0149	0.006	0.1897	-0.0614	0.3013	0.237	-0.0288	-0.2596	-0.0422	0.0577	0.1063	0.2944	-0.0634	0.6171	0.3657	-0.0524	-0.2123	0.0472	0.0815	0.3799	48.7747	-37.9356	9.346
7	-0.0004	-0.0004	-0.0012	0.005	-0.0001	-0.0003	0.0446	-0.0334	-0.0513	0.0161	0.0056	-0.0006	0.0493	-0.024	0.0431	0.4615	-0.2288	-0.2307	0.2015	0.3386	0.4495	35.3427	-50.0487	20.8661
8	0.0962	0.0186	-0.0789	0.0243	-0.0475	0.1127	0.1336	-0.0581	-0.0597	0.0309	0.0219	-0.0031	0.0537	-0.0065	0.1692	0.2959	-0.0798	-0.1703	0.0462	0.0985	0.2843	44.5875	-39.1157	12.0978
9	0.2125	0.0154	-0.1157	0.0075	-0.0014	0.0618	0.1234	-0.1197	-0.0666	0.0056	0.0657	0.0799	0.104	-0.215	0.2049	0.2506	-0.2498	-0.0568	0.3222	0.2311	0.1802	26.4375	-31.5869	22.3573
10	0.0392	0.0116	-0.006	0.0021	-0.0035	0.0327	0.1073	-0.1059	-0.0852	-0.0199	0.0104	0.0603	0.0658	-0.0937	0.1147	0.2936	-0.352	-0.0958	0.3692	0.2304	0.3398	15.4861	-34.3186	11.5299
11	2	9.7514	2	2	2	2	1.8761	-6.826	1.2097	3.2029	-0.3257	-0.1619	-2.3416	2.9455	-1.55	0.4599	0.0234	-0.0516	0.2784	0.0502	0.342	28.0417	-36.8963	7.3392

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 75 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 76 through 245 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 246 through 309 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 310 through 395 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 402 through 402 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 5 through 132 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 133 through 195 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 196 through 245 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 246 through 309 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 310 through 395 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 402 through 402 )

-
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, 2 molecules AB

-
Non-polymers , 5 types, 592 molecules

-
Details

-
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, 2 molecules AB

-Non-polymers , 5 types, 592 molecules

-Details

-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, 2 molecules AB

-
Non-polymers , 5 types, 592 molecules

-
Details

-
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