PDB-6wgy: Crystal structure of a Putative citrate synthase 2 from Mycobacte...

ID or keywords:

Entry

Database: PDB / ID: 6wgy

Title

Crystal structure of a Putative citrate synthase 2 from Mycobacterium bovis in complex with citrate

Components

Putative citrate synthase 2

Keywords

TRANSFERASE / SSGCID / citA / citrate synthase A / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

citrate synthase (unknown stereospecificity) / citrate synthase activity / tricarboxylic acid cycle
Similarity search - Function

Biological species

Mycobacterium bovis (bacteria)

Method

X-RAY DIFFRACTION /

SAD / Resolution: 2.3 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of a Putative citrate synthase 2 from Mycobacterium bovis in complex with citrate
Authors: Abendroth, J. / Yano, J.K. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Apr 6, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 22, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6wgy.cif.gz	699.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6wgy.ent.gz	481.3 KB	Display	PDB format
PDBx/mmJSON format	6wgy.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/wg/6wgy ftp://data.pdbj.org/pub/pdb/validation_reports/wg/6wgy	HTTPS FTP

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Related structure data

Similar structure data	3o8j-2 3o8j-5 1vgm-d 1o7x-1 6aby-d 1vgp-1 5z0q-2 3oqk-d 3o8j-4 6ixl-2 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
Other databases	TargetTrack: MyboA.00896.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#93 - Sep 2007 Citrate Synthase similarity (8) #154 - Oct 2012 Citric Acid Cycle similarity (7)

Deposited unit

A: Putative citrate synthase 2

B: Putative citrate synthase 2

C: Putative citrate synthase 2

D: Putative citrate synthase 2

hetero molecules

179 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative citrate synthase 2

D: Putative citrate synthase 2

hetero molecules

defined by author
Evidence: gel filtration
89.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Putative citrate synthase 2

C: Putative citrate synthase 2

hetero molecules

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

Unit cell

Length a, b, c (Å)	127.140, 153.370, 100.580
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x+1/2,y+1/2,-z #4: -x,-y,z

#1: Protein	Putative citrate synthase 2 Mass: 41076.656 Da / Num. of mol.: 4 / Fragment: MyboA.00896.a.AE1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97) (bacteria) Strain: ATCC BAA-935 / AF2122/97 / Gene: citA, BQ2027_MB0913C / Plasmid: MyboA.00896.a.AE1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21(DE3) References: UniProt: P63778, citrate synthase (unknown stereospecificity)
#2: Chemical	... ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 109 / Source method: obtained synthetically / Formula: I
#3: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 802 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.99 Å³/Da / Density % sol: 58.9 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Micolytic MCSG-1 screen, condition D7: 20% (w/V) PEG 3000, 100mM sodium citrate tribasic / citric acid pH 5.5: MyboA.00896.a.AE1.PS38615 (originally labelled as MythA.10611.a.AE1.PS38615) at ...Details: Micolytic MCSG-1 screen, condition D7: 20% (w/V) PEG 3000, 100mM sodium citrate tribasic / citric acid pH 5.5: MyboA.00896.a.AE1.PS38615 (originally labelled as MythA.10611.a.AE1.PS38615) at 34.35 mg/ml. For phasing the crystal was incubated for 20sec in a mix of 90% reservoir and 10% 2.5M NaI in ethylene glycol, followed by an incubation for 20sec in 80% reservoir and 20% 2.5M NaI in ethylene glycol. The sample was then vitirfied. tray 314035d7: cryo: 20% PEG with 2.5M NaI: puck dvf9-2.

Crystal

Density Matthews: 2.99 Å³/Da / Density % sol: 58.9 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Micolytic MCSG-1 screen, condition D7: 20% (w/V) PEG 3000, 100mM sodium citrate tribasic / citric acid pH 5.5: MyboA.00896.a.AE1.PS38615 (originally labelled as MythA.10611.a.AE1.PS38615) at ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 17, 2020 / Details: RIGAKU VARIMAX HF

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2.3→50 Å / Num. obs: 87868 / % possible obs: 99.9 % / Redundancy: 14.398 % / B_iso Wilson estimate: 46.634 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.093 / R_rim(I) all: 0.097 / Χ²: 1.022 / Net I/σ(I): 19.33

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.3-2.36	14.528	0.64	5.07	6418	0.956	0.663	99.8
2.36-2.42	14.561	0.511	6.22	6267	0.969	0.529	99.9
2.42-2.49	14.562	0.431	7.14	6066	0.976	0.446	99.9
2.49-2.57	14.621	0.36	8.25	5902	0.984	0.373	99.8
2.57-2.66	14.622	0.295	9.64	5805	0.989	0.306	100
2.66-2.75	14.677	0.227	12.06	5511	0.993	0.235	99.9
2.75-2.85	14.699	0.205	12.88	5364	0.994	0.212	99.8
2.85-2.97	14.709	0.163	15.2	5194	0.996	0.168	99.9
2.97-3.1	14.738	0.136	17.53	4968	0.997	0.14	99.9
3.1-3.25	14.74	0.113	20.69	4755	0.998	0.117	99.9
3.25-3.43	14.721	0.095	23.7	4522	0.998	0.099	100
3.43-3.64	14.628	0.079	28.83	4297	0.999	0.082	99.9
3.64-3.89	14.52	0.071	33.05	4063	0.999	0.074	100
3.89-4.2	14.317	0.064	35.87	3776	0.999	0.066	99.7
4.2-4.6	14.158	0.06	38.65	3489	0.999	0.062	99.9
4.6-5.14	13.886	0.059	38.36	3172	0.999	0.062	99.8
5.14-5.94	13.421	0.062	37.55	2825	0.999	0.064	100
5.94-7.27	12.943	0.06	36.74	2402	0.999	0.063	100
7.27-10.29	12.432	0.047	42.72	1902	0.999	0.049	100
10.29-50	10.989	0.05	40.54	1097	0.998	0.053	98

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.18rc4	refinement
PDB_EXTRACT	3.25	data extraction
SHELXDE		phasing
PHASER		phasing
PARROT		phasing
SHELXE		model building
ARP/wARP		model building
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 2.3→47.43 Å / SU ML: 0.269 / Cross valid method: FREE R-VALUE / σ(F): 1.3 / Phase error: 23.6791 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2252	1950	2.22 %	0
R_work	0.1737	-	-	-
obs	0.1748	87847	99.94 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 44.42 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→47.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11061	0	135	802	11998

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0067	11405
X-RAY DIFFRACTION	f_angle_d	0.8132	15596
X-RAY DIFFRACTION	f_chiral_restr	0.0473	1753
X-RAY DIFFRACTION	f_plane_restr	0.0055	2079
X-RAY DIFFRACTION	f_dihedral_angle_d	18.8812	4086

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 (%)
2.3-2.36	0.3057	168	0.2185	6026	X-RAY DIFFRACTION	99.97
2.36-2.42	0.2947	127	0.2056	6039	X-RAY DIFFRACTION	100
2.42-2.49	0.2673	146	0.2	6085	X-RAY DIFFRACTION	99.92
2.49-2.57	0.2489	138	0.192	6065	X-RAY DIFFRACTION	99.94
2.57-2.66	0.2734	132	0.1891	6090	X-RAY DIFFRACTION	100
2.66-2.77	0.2735	158	0.1836	6072	X-RAY DIFFRACTION	99.98
2.77-2.9	0.2765	132	0.1949	6115	X-RAY DIFFRACTION	99.94
2.9-3.05	0.2348	120	0.1925	6123	X-RAY DIFFRACTION	99.98
3.05-3.24	0.2714	121	0.1907	6129	X-RAY DIFFRACTION	99.95
3.24-3.49	0.2863	147	0.1855	6116	X-RAY DIFFRACTION	99.97
3.49-3.84	0.1879	154	0.1578	6155	X-RAY DIFFRACTION	100
3.84-4.4	0.1756	128	0.1448	6185	X-RAY DIFFRACTION	99.92
4.4-5.54	0.1652	143	0.1493	6229	X-RAY DIFFRACTION	99.89
5.54-47.43	0.2169	136	0.176	6468	X-RAY DIFFRACTION	99.74

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	0.686425465579	0.317394778491	0.295546328329	1.63453265633	-0.20662506799	2.72333472567	-0.0370951473013	-0.0348808000597	-0.0765549559182	-0.0547757672065	0.0217929230899	-0.13021864875	-0.0706875695979	0.383043278158	0.0250848158806	0.216447800475	0.0539815192976	-0.00918960458472	0.325428846261	0.00956130625509	0.264023364185	108.184010235	17.1754262902	129.322150848
2	1.63041621714	0.859887431497	0.76442053014	1.2210041389	-0.916996445901	2.69047301835	-0.299392940603	-0.346334177955	-0.000631683428476	0.452120255175	0.163905832344	0.0192101271799	0.154523147514	0.08298194219	0.0906510846891	0.372133823274	0.145901397903	-0.0539544746508	0.35406269572	0.0299497671089	0.297047825331	104.312541039	5.26117594923	141.53385534
3	1.56673332613	-0.751027871298	-0.421532250277	3.04258702535	-0.511790280513	5.36839877703	-0.136856079558	-0.762829879141	-0.269403570887	0.633011621644	0.393028789435	0.594892505505	-0.45411515634	-0.530796152021	-0.27769325888	0.563019352586	0.192797927774	0.0395339634071	0.693542709495	0.0754381130104	0.412465288155	96.6632731936	25.4511776719	156.342713596
4	0.555430673022	0.781913026355	0.125083842081	2.36528333956	-0.101444423126	1.61983584972	-0.114160834873	-0.0941660948391	-0.0967456596843	0.329931732163	0.0343104681177	0.0501398543786	0.27074868432	0.0281700054808	0.0704218058946	0.411464600944	0.169912211841	0.0488018055307	0.399864357959	0.0659961432542	0.359168210453	98.6083534304	-5.88366830687	140.158240452
5	0.840103709575	-0.352709339353	-0.0229424094682	1.08557459562	-0.114894553049	1.7408023592	-0.089136897541	-0.0607465234187	0.0128422129237	-0.00840066953725	0.0361155359502	0.16513223527	-0.106473744075	-0.25737706518	0.0470127501714	0.193764002615	0.0205902357697	-0.0125155405097	0.254807712699	0.0140110121464	0.293571832447	76.5124643397	17.9830309227	105.023132986
6	4.07830069696	1.40460292215	1.06010294503	2.90155589226	3.4678266676	6.68802874625	-0.389165826771	0.111799787653	0.655609200667	-0.885469052723	0.348662820402	-0.471482017785	-0.478379058075	0.813340689346	0.0180757244732	0.530532520401	0.031585141188	-0.0528688250849	0.424434304304	-0.0182246394072	0.567363281516	72.7508512449	45.7432352294	107.653654709
7	1.2122767656	-1.43487611309	-0.731917035683	3.75341089604	1.63771896074	1.55496287324	-0.0731047083635	-0.157518898587	0.067009227988	-0.102503376357	0.193808790989	0.0446260520947	-0.279317144867	-0.1029213281	-0.105095982444	0.239581880619	0.0651279450508	-0.0532790519457	0.343441446182	0.032310633459	0.305692414889	70.2856758653	31.9752363901	107.010267065
8	4.19914781657	0.546645082934	0.520496352485	0.716581768048	-0.409921022744	1.50837266204	-0.0958921644646	0.48590235366	0.267756898612	-0.0794534694936	0.0313591838819	-0.112326421588	-0.0395459690493	0.293317792198	0.0548080972238	0.335430351089	-0.0383099696614	0.0570850913388	0.261586574189	0.00189277485472	0.261690026418	110.15301437	28.378695218	86.2133797097
9	1.65013584326	-0.241258228714	-0.327826707107	1.16139579274	-0.255667910376	2.44552091806	-0.0175277429306	0.0366003908759	-0.0550965945408	-0.116068125994	0.0271647200748	-0.0526509451412	-0.0673936173863	0.182517565889	0.00765932690886	0.206232773529	-0.0201184391144	0.0015270649708	0.179180853238	-0.0120247348321	0.228998310722	105.32060517	19.8543048135	97.332645285
10	1.96086160492	-1.17209960488	-1.00520457919	1.09656248447	0.924846549667	2.3931575901	0.366834097674	0.10532163736	-0.783708976354	-0.308278391674	-0.0364079784563	0.097222837679	0.945504468901	-0.136842391717	-0.0680230965379	0.80369798613	0.13287743135	-0.151065065823	0.206195093016	-0.159611779202	0.608273454925	102.361440766	4.01306317297	86.0782142276
11	0.717797788575	-0.204696835761	0.068550789202	0.801654095355	-0.560073747134	3.17940800526	0.292377752096	0.327885643283	-0.396592817769	-1.03700724276	-0.0799935094407	0.560436820973	0.541136315643	0.175593125647	-0.199489297808	0.878542149642	0.194893069481	-0.199500733896	0.428004664761	-0.114444468416	0.526720318866	109.504863054	5.76225337494	77.8750535106
12	2.45149103809	0.0344843329778	0.0871365134929	0.531962242781	0.210304591765	1.16126983056	-0.0321750827176	0.00165060966924	-0.188885698099	-0.14092298503	-0.00885492006874	0.171002897498	0.0905294906295	-0.298235842815	0.0491512542491	0.270907893535	-0.0158427897156	-0.0464115414817	0.241076525981	0.0539701808612	0.298162184487	82.0151653521	18.9543847024	94.9772482922
13	0.861526535757	0.0613024613539	0.313321905073	1.9302565407	-0.131606980562	1.99931959498	-0.0255885862546	-0.137484104481	-0.132089188091	0.277792117225	0.0598656811836	0.0350409233169	0.22123108413	-0.143625055036	-0.0315222770985	0.310238871064	0.0280729230935	0.0268307401836	0.227450651606	0.0494346205411	0.27941204873	92.6385583596	-10.3146451424	130.193394098
14	4.49114127127	-0.884552829726	0.36910427008	2.60110016141	-1.60951390979	2.90632155272	0.0938405573708	-0.0265636877549	-0.0884412879727	0.0621700191208	-0.150326588543	-0.443643298589	0.252009528603	0.567909830523	0.0385948210348	0.410640434117	0.0205626664701	-0.0739372951629	0.304838727697	-0.0428351998191	0.385168353852	109.982215727	-28.6115822797	124.855680504
15	0.924901996632	0.355409855548	0.666696786857	1.14760531743	0.500698893915	1.48281868353	-0.173564036431	-0.0639769252135	-0.0450811782006	0.0561555173246	0.0759379822098	-0.26298412335	0.09212135943	0.436994590721	0.0532632253045	0.436658332457	0.0713843391536	-0.0459185036553	0.448385982264	0.045475756461	0.339301009472	107.902968069	2.03380332223	140.600040668
16	0.925931810209	0.898016239695	0.426708661378	1.40698786728	0.870615148416	2.309292228	0.132241909084	-0.423403868926	-0.134363000824	0.579838098365	-0.184742064722	-0.28944040321	0.267907179699	0.413088237639	0.0469779056783	0.420851842247	0.15280171752	-0.0585552035232	0.647580833536	0.0485833309499	0.394264473299	112.87238814	8.09382570071	150.154409189

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'C' and (resid 59 through 172 )	C	C	59 - 172	59 - 178
2	2	chain 'C' and (resid 173 through 218 )	C	C	173 - 218	179 - 225
3	3	chain 'C' and (resid 219 through 316 )	C	C	219 - 316	226 - 323
4	4	chain 'C' and (resid 317 through 371 )	C	C	317 - 371	324 - 378
5	5	chain 'D' and (resid 1 through 228 )	D	D	1 - 228	1 - 232
6	6	chain 'D' and (resid 229 through 257 )	D	D	229 - 257	233 - 261
7	7	chain 'D' and (resid 258 through 342 )	D	D	258 - 342	262 - 346
8	8	chain 'D' and (resid 343 through 373 )	D	D	343 - 373	347 - 377
9	9	chain 'A' and (resid 1 through 191 )	A	A	1 - 191	1 - 195
10	10	chain 'A' and (resid 192 through 240 )	A	A	192 - 240	196 - 244
11	11	chain 'A' and (resid 241 through 316 )	A	A	241 - 316	245 - 320
12	12	chain 'A' and (resid 317 through 374 )	A	A	317 - 374	321 - 378
13	13	chain 'B' and (resid 1 through 218 )	B	B	1 - 218	1 - 220
14	14	chain 'B' and (resid 219 through 316 )	B	B	219 - 316	221 - 320
15	15	chain 'B' and (resid 317 through 374 )	B	B	317 - 374	321 - 378
16	16	chain 'C' and (resid 1 through 58 )	C	C	1 - 58	1 - 58

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