PDB-9qct: Crystal structure of Rhizobium etli L-asparaginase ReAV R47A mutant

ID or keywords:

Entry

Database: PDB / ID: 9qct

Title

Crystal structure of Rhizobium etli L-asparaginase ReAV R47A mutant

Components

L-asparaginase II

Keywords

HYDROLASE / Rhizobium etli / amidohydrolases / L-asparaginases / site-directed mutagenesis

Function / homology

L-asparaginase II / L-asparaginase II / L-asparaginase II

Function and homology information

Biological species

Rhizobium etli (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Pokrywka, K. / Grzechowiak, M. / Loch, J.I. / Ruszkowski, M. / Gilski, M. / Jaskolski, M.

Funding support

Poland, 1items

Citation

Journal: To Be Published
Title: Crystal structure of Rhizobium etli L-asparaginase ReAV R47A mutant
Authors: Pokrywka, K. / Grzechowiak, M. / Loch, J.I. / Ruszkowski, M. / Gilski, M. / Jaskolski, M.

History

Deposition	Mar 5, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 16, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9qct.cif.gz	564.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9qct.ent.gz	457.3 KB	Display	PDB format
PDBx/mmJSON format	9qct.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9qct_validation.pdf.gz	472.7 KB	Display	wwPDB validaton report
Full document	9qct_full_validation.pdf.gz	480.9 KB	Display
Data in XML	9qct_validation.xml.gz	75.8 KB	Display
Data in CIF	9qct_validation.cif.gz	105.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qc/9qct ftp://data.pdbj.org/pub/pdb/validation_reports/qc/9qct	HTTPS FTP

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Related structure data

Related structure data	7os3 7os5 7os6 7ou1 7oz6 8cly 8clz 8col 8ori 8osw 8rua 8rud 8rue 8ruf 8rug 9g66 9g67 9g68
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.60884/DZULXI / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: L-asparaginase II

B: L-asparaginase II

C: L-asparaginase II

D: L-asparaginase II

hetero molecules

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

1

A: L-asparaginase II

B: L-asparaginase II

hetero molecules

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

2

C: L-asparaginase II

D: L-asparaginase II

hetero molecules

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

Unit cell

Length a, b, c (Å)	78.059, 91.550, 114.462
Angle α, β, γ (deg.)	90.000, 96.900, 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	L-asparaginase II Mass: 39468.754 Da / Num. of mol.: 4 / Mutation: R47A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium etli (bacteria) / Gene: ansA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RFN5
#2: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1485 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.2 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 22% PEG 4000, 0.2 M MgCl2, 0.1 M Bicine pH 9.0, 1% v/v isopropanol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.75→71.29 Å / Num. obs: 160568 / % possible obs: 99.6 % / Redundancy: 3.5 % / B_iso Wilson estimate: 18.87 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.115 / R_rim(I) all: 0.135 / Net I/σ(I): 8.38
Reflection shell	Resolution: 1.75→1.86 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.892 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 25814 / CC_1/2: 0.57 / R_rim(I) all: 1.057

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.75→50.6 Å / SU ML: 0.2189 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.4211
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2109	1001	0.62 %
R_work	0.1709	159484	-
obs	0.1712	160485	99.54 %

Solvent computation

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

Displacement parameters

B_iso mean: 22.08 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→50.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10316	0	113	1485	11914

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0119	10864
X-RAY DIFFRACTION	f_angle_d	1.106	14688
X-RAY DIFFRACTION	f_chiral_restr	0.0693	1632
X-RAY DIFFRACTION	f_plane_restr	0.0107	1953
X-RAY DIFFRACTION	f_dihedral_angle_d	13.3105	4060

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 (%)
1.75-1.84	0.3084	142	0.2751	22568	X-RAY DIFFRACTION	98.99
1.84-1.96	0.2886	143	0.2296	22792	X-RAY DIFFRACTION	99.88
1.96-2.11	0.2318	142	0.1899	22747	X-RAY DIFFRACTION	99.8
2.11-2.32	0.2358	143	0.17	22810	X-RAY DIFFRACTION	99.81
2.32-2.66	0.2164	143	0.1637	22783	X-RAY DIFFRACTION	99.68
2.66-3.35	0.2164	143	0.1632	22858	X-RAY DIFFRACTION	99.69
3.35-50.6	0.1603	145	0.1434	22926	X-RAY DIFFRACTION	98.92

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	0.954325795635	1.94031351509	-0.198817740464	5.10424355857	-0.868866278885	1.22741767846	-0.0469746480504	0.105615090748	-0.0351070353178	-0.0510576691868	0.0688768105255	0.141408392986	-0.0329677548709	0.0231076810428	-0.027808677654	0.0939385705769	0.00745239335694	-0.00663711342309	0.132480471534	-0.00417843672574	0.10741392539	-9.06037289028	46.8597957083	-7.89283197865
2	0.962878055653	0.160330333321	-0.321472970254	1.08895163166	-0.457880243664	1.93354977905	0.0236981832208	-0.0493615105425	0.0325199280123	0.0894938220837	-0.00563824666139	0.0506040546674	-0.0273430651228	-0.0518620061562	-0.022296305707	0.133455443192	-0.0166210177777	-0.00948492938393	0.114997357297	-0.00195708565992	0.153231950995	-4.27880043176	66.0490945587	14.9402699134
3	2.43465925033	-0.687160470953	0.147428452312	1.40557731365	0.122600115369	1.35671833961	-0.0127135613386	0.0554248156474	-0.0241149942993	-0.011926632734	0.0113501628338	-0.118584197398	-0.0412412627987	0.168932352768	0.00640667285583	0.123326490701	-0.0362140683725	0.0137437403552	0.111798235477	0.00291766779383	0.167979485188	3.25881960249	62.4235066013	0.361684985778
4	0.800697168275	0.588143888605	0.321690108311	1.00538330401	0.152702240261	0.42471825303	-0.00754966732591	0.0257258826948	-0.129619860789	0.0405702697807	0.0201211118772	-0.125920685448	0.0571769317638	0.0292369302915	-0.00153866136111	0.112813367736	0.0147673907564	0.00717012676064	0.119990338504	-0.0094507340755	0.175744699082	-2.10999300421	43.760601183	2.86251952228
5	7.67325446511	7.45756506604	1.23029355027	7.51612088936	1.3989923622	1.02911396325	-0.165598354709	0.19482898079	0.150241333149	-0.169983200433	0.127300425092	0.0586461898045	-0.0332356553018	-0.0231543006075	0.0317393072969	0.110790077373	0.010560077144	-0.0169270127643	0.141555581218	0.0155706099072	0.165094462728	-25.3160915832	51.7175060273	-6.79771829724
6	0.428590209503	0.418931474692	-0.522274515796	1.10526703478	-0.784471616247	0.749578227778	-0.046014235411	0.0775304258772	-0.030970730659	-0.0225919304919	0.0474399566699	0.100450722795	0.0578809519992	-0.130551296668	-0.0144187285139	0.130123797517	-0.0429799964801	-0.0109097935622	0.185340906012	-0.033318423109	0.169887370344	-40.1398680703	31.6131809769	0.810802335337
7	2.57673129953	0.611970678366	0.20936503899	2.84539231716	0.377185402182	1.77121495998	0.031208995999	-0.0446811309976	0.052285591271	0.168164251044	-0.0133411049228	-0.16594054055	-0.0563799630757	0.115444906157	-0.0300760523008	0.139108406497	-0.0255038675156	0.00440067022787	0.135295080255	0.00518904051998	0.10010694383	-33.7464007747	30.8656956494	19.3082872915
8	1.43869355636	-1.03242242779	0.582948850319	1.6057922183	-1.07252227866	1.47943988213	-0.0123752205574	0.0941483101799	-0.0200643922534	-0.176601054296	-0.0185770247456	-0.0017290311026	0.229118131762	-0.126125879763	0.0388296855164	0.158504524284	-0.0720258792875	0.00183995177045	0.162813250436	-0.0328853657335	0.14545242093	-37.8538757788	27.7793691123	-0.921261953731
9	1.98129980304	0.602028293378	0.27135892479	3.35044991822	0.0986444049231	1.25163028658	-0.0431841674402	0.0765535265881	-0.0627898213842	0.0542326157961	0.0141060869304	0.282066062868	0.0383175906314	-0.388354586879	0.0650528444601	0.109051409481	-0.0196856785212	0.0258443502895	0.233057695832	0.00128860004999	0.176513732621	-46.3266714138	39.819382433	7.6571656065
10	4.44532726135	0.532455189787	0.71727886936	2.19732973726	0.260097038817	1.46180512982	-0.0612085218433	0.149746310324	0.0434312943994	-0.0701577960357	0.0792064848204	0.0545654702401	-0.0353593593615	-0.14779400658	-0.0120131534626	0.101446614396	-0.00102647443963	0.0092434262428	0.155624440686	0.0257839263528	0.109014185365	-38.7260385303	46.5232754724	-3.32417275274
11	2.36894583589	1.54368755317	1.24470849668	1.94019877926	1.44775328262	1.89973019206	-0.0157070636427	-0.116767025618	0.0511961042149	-0.0269600161586	0.0396696988835	0.100704656416	-0.0724432870672	-0.0649616235533	-0.0178344533652	0.163612026815	0.0291882505434	-0.0216033526154	0.118805864567	0.0329622952497	0.219964697643	-32.9770332656	58.1239094285	1.02639507114
12	2.96411508442	-2.39258151875	-0.684093463325	4.04729155452	0.850881268666	1.05745220603	-0.0701121090185	-0.102606839144	-0.123909105423	0.0988465081701	0.0276141362447	0.0863380055744	-0.0067644986161	-0.0117670313861	0.0422361343743	0.116695220184	-0.0133397728269	-0.00292176414376	0.128633233532	0.00615686949264	0.101731651416	2.25590477595	44.3283711538	64.5272247944
13	2.28231883393	-0.69943877325	-0.776786330063	1.19562857627	0.621005620714	1.51996821111	0.0198989526827	0.103143594309	-0.0165861390242	-0.0375439152573	-0.0606145638002	0.0490208823099	-0.00116768590639	-0.0703854983761	0.0465538263972	0.142371385337	0.00501774548022	-0.00977520350869	0.100228901918	0.00524766231836	0.113366249838	-4.8139173507	63.0768941064	40.2323587434
14	3.57293157357	-1.86125525182	-1.583913134	5.33073436176	1.98857582774	3.40368844437	0.177235190422	0.261722652556	-0.266025669034	-0.283755394852	-0.153644127612	-0.189449900335	0.0442120710119	0.227278124067	-0.0176490722085	0.163795800116	0.0211092505374	-0.0259012256346	0.198072408202	-0.00734060119991	0.139675721168	3.33142844686	59.1349188099	36.9036119643
15	0.596616134734	0.0243065814254	-0.177623501079	1.19472701411	-0.0637893929406	0.781230329453	-0.00965771812234	-0.0019656143488	0.0278986790161	0.00731052683752	0.00803012617695	0.0527634366298	-0.0205000219434	-0.0293703899718	0.000831692947006	0.141044127843	0.0168506564293	2.02079854324E-5	0.13955647324	0.00382162606134	0.158769402906	-7.73342646221	60.2125215341	52.850859233
16	2.54147504368	-0.877048708599	-0.571482038242	1.4832677306	0.305780003966	0.851981965877	-0.0573176216365	0.0600152012376	-0.106889762044	0.0272787226186	0.0207864714363	0.146982450761	0.064899906115	-0.0361422389292	0.0491905519587	0.11783093216	-0.00542960152547	0.000767914472889	0.102040889055	0.0142483588649	0.142954870184	-3.81043617816	39.680076391	56.6147264854
17	4.27581214935	-5.65381315639	1.90687790494	7.54450907343	-2.49375896198	0.8585688629	-0.124292227994	-0.108522008205	-0.0208850588739	0.211578726642	0.152917091765	0.149459874642	-0.074315089318	0.0288518523324	-0.032421214181	0.153912597876	-0.00528546376089	0.00105733057321	0.187270662712	-0.00686343286548	0.180808062439	18.6262167141	49.2049989321	63.3830621698
18	0.58257909411	-1.0629258901	-1.13760328054	2.4022961335	1.90864516419	2.62264422555	-0.0186317453513	-0.0268184854705	0.0145953980923	0.0156277534432	0.0346886579136	-0.0625385376404	0.0175049597807	0.133057661165	-0.0271014684798	0.126853986089	0.00601898769102	-0.00653675179308	0.179570834	0.0330902066988	0.147826698043	32.9248885996	28.3954789443	55.8807140045
19	2.37791940812	0.0906900378658	-0.0732858242812	1.79990892929	-0.181107142783	1.81409400444	-0.0140634905376	0.102444297523	0.186842192363	-0.153863810446	-0.0522950703875	0.151122118534	-0.163536508783	-0.122292494264	0.0436441650237	0.18199152936	0.0370897188288	-0.00606242759283	0.139597720476	0.0181762461556	0.122118343997	26.1082861817	32.0728010891	35.4091520311
20	0.562033199568	0.154204247589	-0.148842338964	1.14333957653	0.231760521644	0.979691130918	-0.0128887307567	-0.0419469853019	0.0123888172242	-0.0270550193333	0.0149689981241	-0.117445008329	0.0337153162584	0.0930844927496	-5.86245630638E-5	0.119663720449	0.0202874533303	-0.00185231469363	0.162029127998	0.0178011097289	0.154709242717	33.3127044723	27.5800921605	51.3982880595
21	5.61943181729	-0.799417371143	0.751602921482	1.79001010715	0.0716371057661	1.32990917189	-0.0125448196834	-0.166350405714	-0.0619230546542	0.0551210345133	0.050562764926	-0.206836777483	-0.0675163324696	0.145347071982	-0.0358567234055	0.109117728945	-0.00434858509732	0.00643917662324	0.148059228212	-0.013747214055	0.146087284437	31.7861253482	43.482446263	59.9001879877
22	3.33218824962	-2.33083701965	1.92313311142	2.41104726322	-1.25969589008	2.28391067768	0.015871943414	0.156777624075	0.254910622501	-0.00221423110531	-0.00335896278014	-0.234749067386	-0.0384421448314	0.0457522239591	-0.00206934309733	0.166813248306	-0.0359681493311	-0.00258550326171	0.119847342273	-0.0105960008149	0.206136230624	26.0138195071	55.4590224628	55.4025189752

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 4 through 46 )	A	A	4 - 46	1 - 43
2	2	chain 'A' and (resid 47 through 175 )	A	A	47 - 175	44 - 172
3	3	chain 'A' and (resid 176 through 237 )	A	A	176 - 237	173 - 234
4	4	chain 'A' and (resid 238 through 352 )	A	A	238 - 352	235 - 349
5	5	chain 'B' and (resid 4 through 28 )	B	H	4 - 28	1 - 25
6	6	chain 'B' and (resid 29 through 70 )	B	H	29 - 70	26 - 67
7	7	chain 'B' and (resid 71 through 161 )	B	H	71 - 161	68 - 158
8	8	chain 'B' and (resid 162 through 216 )	B	H	162 - 216	159 - 213
9	9	chain 'B' and (resid 217 through 265 )	B	H	217 - 265	214 - 262
10	10	chain 'B' and (resid 266 through 313 )	B	H	266 - 313	263 - 310
11	11	chain 'B' and (resid 314 through 352 )	B	H	314 - 352	311 - 349
12	12	chain 'C' and (resid 4 through 46 )	C	R	4 - 46	1 - 43
13	13	chain 'C' and (resid 47 through 114 )	C	R	47 - 114	44 - 111
14	14	chain 'C' and (resid 115 through 149 )	C	R	115 - 149	112 - 146
15	15	chain 'C' and (resid 150 through 265 )	C	R	150 - 265	147 - 262
16	16	chain 'C' and (resid 266 through 352 )	C	R	266 - 352	263 - 349
17	17	chain 'D' and (resid 4 through 28 )	D	Z	4 - 28	1 - 25
18	18	chain 'D' and (resid 29 through 70 )	D	Z	29 - 70	26 - 67
19	19	chain 'D' and (resid 71 through 135 )	D	Z	71 - 135	68 - 132
20	20	chain 'D' and (resid 136 through 265 )	D	Z	136 - 265	133 - 262
21	21	chain 'D' and (resid 266 through 314 )	D	Z	266 - 314	263 - 311
22	22	chain 'D' and (resid 315 through 352 )	D	Z	315 - 352	312 - 349

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

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