PDB-7kno: Crystal structure of Acetyl-CoA synthetase in complex with adenos...

ID or keywords:

Entry

Database: PDB / ID: 7kno

Title

Crystal structure of Acetyl-CoA synthetase in complex with adenosine-5'-ethylphosphate from Cryptococcus neoformans var. grubii serotype A (H99)

Components

Acetyl-coenzyme A synthetase

Keywords

LIGASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / AMP binding / ATP binding / metal ion binding / cytosol
Similarity search - Function

Biological species

Cryptococcus neoformans var. grubii serotype A (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of Acetyl-CoA synthetase in complex with adenosine-5'-ethylphosphate from Cryptococcus neoformans var. grubii serotype A (H99)
Authors: Abendroth, J. / DeBouver, N.D. / Fox III, D. / Esan, T.E. / Hagen, T.J. / Krysan, D.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Nov 5, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 30, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7kno.cif.gz	957.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7kno.ent.gz	655.2 KB	Display	PDB format
PDBx/mmJSON format	7kno.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7kno_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	7kno_full_validation.pdf.gz	1.5 MB	Display
Data in XML	7kno_validation.xml.gz	83.9 KB	Display
Data in CIF	7kno_validation.cif.gz	128.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kn/7kno ftp://data.pdbj.org/pub/pdb/validation_reports/kn/7kno	HTTPS FTP

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Related structure data

Related structure data	5ifiS S: Starting model for refinement
Similar structure data	5k85-d 7l4g-d 5ifi-d 7knp-d 5u29-d 3v4x-d 5xmj-1 5m1b-d 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: SSGCID-CrneC.00629.a.FS11

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#78 - Jun 2006 Luciferase similarity (6)

Deposited unit

A: Acetyl-coenzyme A synthetase

B: Acetyl-coenzyme A synthetase

C: Acetyl-coenzyme A synthetase

hetero molecules

235 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	72.690, 184.700, 84.840
Angle α, β, γ (deg.)	90.000, 93.869, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Acetyl-coenzyme A synthetase Mass: 77475.750 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus) Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_00797 / Plasmid: Crnec.00629.a.FS11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: J9VFT1, acetate-CoA ligase
#2: Chemical	ChemComp-WTA / 5'-O-[(S)-ethoxy(hydroxy)phosphoryl]adenosine Mass: 375.274 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₂H₁₈N₅O₇P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1735 / 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: 2.45 Å³/Da / Density % sol: 49.8 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: Optimization screen around RigakuReagents Wizard screen 1/2, condition e8: 100mM potassium / sodium phosphate dibasic pH 6.2, 200mM NaCl 13.18% (w/V) PEG 8000: CrneC.00629.a.FS11.PD00460 at ...Details: Optimization screen around RigakuReagents Wizard screen 1/2, condition e8: 100mM potassium / sodium phosphate dibasic pH 6.2, 200mM NaCl 13.18% (w/V) PEG 8000: CrneC.00629.a.FS11.PD00460 at 10mg/ml + ethyl-AMP + AcCoA: tray 317932 c7: cryo: 20% EG + compounds: puck: fgi6-9

Crystal

Density Matthews: 2.45 Å³/Da / Density % sol: 49.8 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: Optimization screen around RigakuReagents Wizard screen 1/2, condition e8: 100mM potassium / sodium phosphate dibasic pH 6.2, 200mM NaCl 13.18% (w/V) PEG 8000: CrneC.00629.a.FS11.PD00460 at ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 24, 2020 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.8→50 Å / Num. obs: 205272 / % possible obs: 99.8 % / Redundancy: 3.78 % / B_iso Wilson estimate: 32.568 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.052 / R_rim(I) all: 0.06 / Χ²: 0.928 / Net I/σ(I): 15.12

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
1.8-1.85	3.627	0.515	2.31	15138	0.849	0.605	99.9
1.85-1.9	3.794	0.412	2.99	14811	0.902	0.48	99.9
1.9-1.95	3.797	0.32	3.89	14342	0.933	0.373	99.9
1.95-2.01	3.806	0.262	4.77	14023	0.951	0.305	99.9
2.01-2.08	3.807	0.206	6.05	13547	0.968	0.24	99.9
2.08-2.15	3.818	0.163	7.5	13045	0.979	0.19	99.9
2.15-2.23	3.819	0.126	9.6	12643	0.986	0.146	99.9
2.23-2.32	3.813	0.106	11.28	12165	0.989	0.124	99.8
2.32-2.43	3.817	0.087	13.43	11703	0.993	0.102	99.8
2.43-2.55	3.813	0.074	15.57	11097	0.994	0.086	99.9
2.55-2.68	3.805	0.063	18.14	10653	0.995	0.073	99.9
2.68-2.85	3.792	0.053	21.03	9998	0.997	0.062	99.8
2.85-3.04	3.772	0.044	24.47	9451	0.997	0.052	99.8
3.04-3.29	3.757	0.038	28.84	8784	0.998	0.044	99.8
3.29-3.6	3.747	0.033	32.82	8051	0.998	0.038	99.7
3.6-4.02	3.747	0.03	35.74	7337	0.998	0.035	99.7
4.02-4.65	3.762	0.029	38.25	6437	0.998	0.034	99.8
4.65-5.69	3.773	0.029	38.79	5486	0.998	0.033	99.9
5.69-8.05	3.775	0.03	38.88	4232	0.998	0.035	99.8
8.05-50	3.565	0.03	40.58	2329	0.998	0.036	98.1

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Processing

Software

Name	Version	Classification
PHENIX	1.19rc4 4035	refinement
XDS		data reduction
XSCALE		data scaling
PDB_EXTRACT	3.27	data extraction
MoRDa		phasing
PHASER		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 5ifi

5ifi

Resolution: 1.8→46.94 Å / SU ML: 0.2077 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.426
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1898	2070	1.01 %	0
R_work	0.1637	203120	-	-
obs	0.164	205190	99.84 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 37.97 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→46.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14797	0	132	1735	16664

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0082	15549
X-RAY DIFFRACTION	f_angle_d	0.9141	21254
X-RAY DIFFRACTION	f_chiral_restr	0.0615	2307
X-RAY DIFFRACTION	f_plane_restr	0.0095	2752
X-RAY DIFFRACTION	f_dihedral_angle_d	12.8185	5590

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 (%)
1.8-1.84	0.2925	157	0.2711	13466	X-RAY DIFFRACTION	99.79
1.84-1.89	0.2532	148	0.2341	13511	X-RAY DIFFRACTION	99.88
1.89-1.94	0.2269	154	0.2054	13445	X-RAY DIFFRACTION	99.9
1.94-2	0.2187	167	0.1904	13538	X-RAY DIFFRACTION	99.9
2-2.06	0.2198	131	0.1863	13556	X-RAY DIFFRACTION	99.94
2.06-2.13	0.2304	132	0.1873	13563	X-RAY DIFFRACTION	99.92
2.13-2.22	0.2337	143	0.1739	13543	X-RAY DIFFRACTION	99.95
2.22-2.32	0.2086	102	0.17	13492	X-RAY DIFFRACTION	99.84
2.32-2.44	0.2132	120	0.1704	13589	X-RAY DIFFRACTION	99.88
2.44-2.6	0.2284	123	0.1686	13567	X-RAY DIFFRACTION	99.87
2.6-2.8	0.1878	119	0.1709	13561	X-RAY DIFFRACTION	99.88
2.8-3.08	0.2458	114	0.1686	13541	X-RAY DIFFRACTION	99.81
3.08-3.52	0.17	143	0.1548	13559	X-RAY DIFFRACTION	99.7
3.52-4.44	0.1586	154	0.1341	13570	X-RAY DIFFRACTION	99.75
4.44-46.94	0.1483	163	0.1452	13619	X-RAY DIFFRACTION	99.57

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	0.937373726407	-0.478078624041	0.248499462049	0.863713732196	-0.559128648871	0.630772654297	0.0255159488731	-0.0367665856203	-0.107398282081	-0.130244561729	0.20581843672	0.437770316644	0.11921968727	-0.235870150005	-0.145806611412	0.154181119463	-0.0352667576894	-0.027415674363	0.275024119505	0.0782474755527	0.294296311016	-20.6785337477	3.16495980867	-8.38998995232
2	0.938267073646	-0.654801501539	0.465234729308	1.64215770985	-0.879404719645	1.06926095381	0.183571151393	0.167008101029	-0.159217955768	-0.500509635343	0.0110884756226	0.223829188435	0.390167634342	0.0282593219546	-0.130136082414	0.269907123675	-0.00864277447757	-0.0469712476881	0.206184475272	-0.0216581363344	0.174176317881	-8.48033983511	-7.67361428003	-17.4011025237
3	0.947898605201	0.261196784473	0.288410211494	2.017501258	-0.332773574914	1.48971821319	-0.0130818977286	0.0292451241491	0.06077002632	-0.264058453511	0.0850550990553	0.263329395044	-0.0276075729337	-0.115562542768	-0.0669450530244	0.136336724958	-0.0070855538606	0.0018835563375	0.198494364269	0.0365899943083	0.197930452211	-17.3841150089	17.2870503027	-22.7072513962
4	2.12817911847	0.609088044324	0.643536594873	1.06792654287	1.74162674359	2.91399188783	0.0205179127881	0.484435437152	-0.105523626179	-0.921450960201	0.211892687367	0.231925878058	0.0923949915699	-0.0795276273815	-0.200818538568	0.792265838956	-0.0698623509175	-0.270396383923	0.420017136739	0.033883639476	0.383765346994	-22.7940048708	5.69955693627	-46.8315315069
5	5.80420438142	-0.522950810268	3.54722044208	3.36201089592	-0.973041426947	2.77508778798	0.0385639891194	0.470591374196	-0.345609283599	-0.651460952874	-0.050085310559	-0.405440056448	0.832528414317	0.521874063156	-0.0670097492444	0.687271964537	0.0552847384787	0.0155759719036	0.506283201344	-0.0187133971671	0.351039784544	-6.87232282225	2.0371233721	-40.8033519266
6	0.654225168357	-0.347485261938	0.356019961514	1.88382635094	-0.609717322846	0.690725290923	-0.145468630918	-0.103652385566	0.0108661235912	0.473674875278	0.147808412814	-0.0306055418713	-0.127148643993	-0.0763356474821	3.23205696739E-5	0.257160555732	0.0665612613415	0.0171561166246	0.204194076793	-0.0262057292521	0.0991800740935	12.7871903037	-20.4267642389	23.3644557837
7	2.01485019073	0.189841974725	0.183552386939	4.03197768966	-0.369908861294	2.0783688594	-0.0872123949715	0.11623506785	0.00876685897017	0.00741611103265	0.0783104533099	-0.768618577437	-0.231290368668	0.260964839129	0.0345642588975	0.224291140397	-0.00175082440618	0.0287940079377	0.22160971404	-0.0423563024493	0.308478910513	23.2607467533	-47.5651050311	23.566201342
8	0.860136044508	0.0402103451649	0.27821609435	0.220608590613	0.243293620425	0.47411763568	-0.447700199971	-0.331577569997	0.634883788668	0.723201389199	0.0677144817738	-0.276106083281	-0.656300206534	-0.176372222238	0.150557952435	0.750448657194	0.163798445242	-0.270806433887	0.304415169139	-0.186107185608	0.469910062455	5.36798143859	26.6420716751	18.8123083548
9	1.0126543339	0.0658039897402	0.10602899145	0.140457737807	-0.142177050734	0.471405696753	-0.298248618279	0.257991930059	0.585823257877	0.241025349069	-0.194045459572	-0.500867924696	-0.38900359635	0.266131062421	0.220043633177	0.184206085161	-0.101320257041	-0.118061395006	0.322847892763	0.196714988666	0.592901513679	18.5483230079	21.8785547119	-5.23188378292
10	0.276073732995	0.0492040513222	0.0874788404497	1.29634667057	-0.248231179449	0.722178649834	-0.410430507942	-0.107069334023	0.68506373974	0.420472481673	-0.08926779105	-0.343344596031	-0.776150696604	0.156000822023	0.0767215401673	0.680533654892	-0.0316363827536	-0.412766935963	0.152969439823	-0.0332620466381	0.711854299908	13.8119039252	32.6393064435	10.2387009407
11	0.619033189989	0.425436416835	0.207890326922	0.360736746755	0.179775382898	0.0826998082772	-0.167665267426	-0.0368188181159	0.505039341428	0.145287559524	-0.0399977537117	-0.155483725974	-0.558429943888	0.110223843487	0.23298502131	1.28544996333	-0.0963615620152	-0.588840047592	0.28047448198	-0.137906375525	1.07459579002	16.840745194	49.8303484155	15.5008482688
12	0.513053662838	0.189508916536	0.0896220178827	0.820931121411	0.29346603347	0.709763743767	-0.285405604171	-0.545608541526	0.53013995472	0.468196989414	-0.102519518712	-0.360805266323	-0.639591801167	0.274978531784	-0.539805029729	0.960716942499	-0.0516921743726	-0.776361912466	0.324420742615	-0.309422715838	0.651733854452	23.0359600886	27.9799198525	27.5248851054
13	1.43364471833	1.63252203698	-1.24259694201	4.13769987343	-0.56970492025	3.58720370784	-0.033354979977	0.0352788504388	0.559446733957	-0.0781258626837	0.078031510988	-0.242221359305	-0.0969528515234	0.491186668708	-0.0498488701329	0.752747751599	-0.0349693873053	-0.0191592496199	0.934338280214	-0.0335054999853	0.98425963454	46.3929192267	31.9210938149	10.5386016021
14	0.073691900091	0.475455646974	0.247660970352	4.09639643945	0.0406212335393	5.5664680726	-0.209149957936	0.325445007958	0.765183339702	-0.233919449774	-0.0210348598624	0.0188654015232	-0.604381922352	0.877348370712	0.210480880431	0.639403227655	-0.0766959572084	-0.0796760352021	0.802864977632	0.00151091340165	1.04192228331	44.5259697489	36.9432099965	6.04303682549

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 'A' and (resid 10 through 132 )	A	A	10 - 132	1 - 123
2	2	chain 'A' and (resid 133 through 453 )	A	A	133 - 453	124 - 442
3	3	chain 'A' and (resid 454 through 555 )	A	A	454 - 555	443 - 544
4	4	chain 'A' and (resid 556 through 629 )	A	A	556 - 629	545 - 618
5	5	chain 'A' and (resid 630 through 677 )	A	A	630 - 677	619 - 666
6	6	chain 'B' and (resid 10 through 555 )	B	G	10 - 555	1 - 542
7	7	chain 'B' and (resid 556 through 677 )	B	G	556 - 677	543 - 664
8	8	chain 'C' and (resid 25 through 132 )	C	N	25 - 132	1 - 108
9	9	chain 'C' and (resid 133 through 278 )	C	N	133 - 278	109 - 254
10	10	chain 'C' and (resid 279 through 382 )	C	N	279 - 382	255 - 358
11	11	chain 'C' and (resid 383 through 432 )	C	N	383 - 432	359 - 408
12	12	chain 'C' and (resid 433 through 551 )	C	N	433 - 551	409 - 527
13	13	chain 'C' and (resid 552 through 602 )	C	N	552 - 602	528 - 564
14	14	chain 'C' and (resid 603 through 633 )	C	N	603 - 633	565 - 595

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-Structure viewers

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-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

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-Assembly

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-Experimental details

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-Data collection

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+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

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Movie

-
Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

-
Validation report

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Related structure data

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Links

-
Assembly

-
Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi