PDB-9yzw: Joint Xray/Neutron structure of Escherichia coli YajL at room tem...

ID or keywords:

Entry

Database: PDB / ID: 9yzw

Title

Joint Xray/Neutron structure of Escherichia coli YajL at room temperature

Components

Chaperone YajL

Keywords

HYDROLASE / DJ-1 superfamily / Cysteine dependent enzyme

Function / homology

Function and homology information

protein deglycase / protein deglycase activity / DNA repair / cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION / NEUTRON DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Lin, J. / Kovalevsky, A. / Walker, A.R. / Wilson, M.A.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Environmental contributions to proton sharing in protein low barrier hydrogen bonds
Authors: Lin, J. / Gerlits, O. / Kneller, D.W. / Weiss, K.L. / Coates, L. / Hix, M.A. / Effah, S.Y. / Kovalevsky, A. / Walker, A.R. / Wilson, M.A.

#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...

History

Deposition	Oct 30, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 19, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9yzw.cif.gz	272.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9yzw.ent.gz	221.3 KB	Display	PDB format
PDBx/mmJSON format	9yzw.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/yz/9yzw ftp://data.pdbj.org/pub/pdb/validation_reports/yz/9yzw	HTTPS FTP

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Related structure data

Related structure data	9yfrC 9yfsC 9ygwC 9ygxC 9yh8C 9ykfC 9yzvC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: Chaperone YajL

B: Chaperone YajL

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	44.289, 79.303, 100.183
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Chaperone YajL / DJ-1 family protein / Oxidative-stress-resistance chaperone Mass: 21080.318 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: thiJ, ACU57_11870, AM266_04520, ERS085365_02411, ERS085416_01937, ERS139211_01908, ERS150873_01827, PU15_11320, PU38_04800, SK85_00449 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8T6D9
#2: Chemical	ChemComp-D8U / deuterium(1+) Mass: 2.014 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: D / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment

Method	Number of used crystals
X-RAY DIFFRACTION	1
NEUTRON DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.09 Å³/Da / Density % sol: 41.05 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 100 mM Tris pH=8.0, 250 mM MgCl2 and 20% PEG 4000

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	293	1	N
2	293	1	N

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
ROTATING ANODE			RIGAKU MICROMAX-007 HF	1	1.542
SPALLATION SOURCE	ORNL Spallation Neutron Source	MANDI		2	2.00-4.16

Detector

Type	ID	Detector	Date
DECTRIS EIGER2 R 4M	1	PIXEL	Sep 20, 2021
ORNL ANGER CAMERA	2	SCINTILLATION	Sep 7, 2021

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	LAUE	L	neutron	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.542	1
2	2	1
3	4.16	1

Reflection

B_iso Wilson estimate: 15.91 Å² / Entry-ID: 9YZW

Resolution (Å)	Num. obs	% possible obs (%)	Redundancy (%)	CC_1/2	Diffraction-ID	Net I/σ(I)
1.65-100.18	43186	99.7	8.9	0.995	1	26.96
1.79-14.61	32647	97.1	6.9	0.905	2	12.7

Reflection shell

Resolution (Å)	Num. unique obs	CC_1/2	Diffraction-ID
1.65-1.71	4304	0.738	1
1.79-1.86	2863	0.604	2

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Processing

Software

Name: PHENIX / Version: 1.19.2_4158 / Classification: refinement

Refinement

SU ML: 0.1396 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 16.3973 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)	Refine-ID	B_iso mean (Å²)	R_factor R_free	R_factor R_work	R_factor obs	Num. reflection R_free	Num. reflection R_work	Num. reflection obs	% reflection R_free (%)	% reflection obs (%)	σ(F)	Diffraction-ID
1.65-25.56	X-RAY DIFFRACTION	25.26	0.1642	0.1371	0.1385	2215	40869	43084	5.14	99.64	1.34
1.79-14.6	NEUTRON DIFFRACTION		0.2226	0.1774				32639		96.73		2

Refinement step

Cycle: LAST / Resolution: 1.65→25.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2902	0	0	181	3083

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	7313
X-RAY DIFFRACTION	f_angle_d	1.223	12905
X-RAY DIFFRACTION	f_dihedral_angle_d	16.752	1897
X-RAY DIFFRACTION	f_chiral_restr	0.072	527
X-RAY DIFFRACTION	f_plane_restr	0.007	1379
NEUTRON DIFFRACTION	f_bond_d	0.009	7313
NEUTRON DIFFRACTION	f_angle_d	1.223	12905
NEUTRON DIFFRACTION	f_dihedral_angle_d	16.752	1897
NEUTRON DIFFRACTION	f_chiral_restr	0.072	527
NEUTRON DIFFRACTION	f_plane_restr	0.007	1379

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 (%)
1.65-1.69	0.2715	121	0.2389	2498	X-RAY DIFFRACTION	99
1.69-1.73	0.2276	153	0.2144	2484	X-RAY DIFFRACTION	99
1.73-1.77	0.2453	140	0.1957	2536	X-RAY DIFFRACTION	99
1.77-1.82	0.2295	133	0.1829	2475	X-RAY DIFFRACTION	99
1.82-1.87	0.2156	153	0.1641	2508	X-RAY DIFFRACTION	99
1.87-1.93	0.1813	133	0.1423	2546	X-RAY DIFFRACTION	99
1.93-2	0.1573	133	0.1301	2506	X-RAY DIFFRACTION	99
2-2.08	0.1497	133	0.129	2525	X-RAY DIFFRACTION	100
2.08-2.17	0.1649	159	0.1344	2506	X-RAY DIFFRACTION	100
2.17-2.29	0.1538	119	0.1216	2602	X-RAY DIFFRACTION	100
2.29-2.43	0.1489	132	0.1192	2565	X-RAY DIFFRACTION	100
2.43-2.62	0.1521	130	0.1294	2585	X-RAY DIFFRACTION	100
2.62-2.88	0.1841	142	0.14	2569	X-RAY DIFFRACTION	100
2.88-3.3	0.1762	140	0.1427	2595	X-RAY DIFFRACTION	100
3.3-4.15	0.1334	146	0.1163	2624	X-RAY DIFFRACTION	100
4.15-25.56	0.1332	148	0.1252	2745	X-RAY DIFFRACTION	100
1.79-1.85	0.3117	121	0.2939	2152	NEUTRON DIFFRACTION	81
1.85-1.91	0.2913	134	0.2475	2460	NEUTRON DIFFRACTION	95
1.91-1.97	0.2523	134	0.211	2553	NEUTRON DIFFRACTION	97
1.97-2.05	0.2254	137	0.1751	2571	NEUTRON DIFFRACTION	98
2.05-2.15	0.2379	160	0.1596	2580	NEUTRON DIFFRACTION	98
2.15-2.26	0.1909	126	0.1424	2628	NEUTRON DIFFRACTION	99
2.26-2.4	0.2043	131	0.1449	2655	NEUTRON DIFFRACTION	100
2.4-2.58	0.211	137	0.1551	2658	NEUTRON DIFFRACTION	100
2.58-2.84	0.1925	134	0.1578	2667	NEUTRON DIFFRACTION	99
2.84-3.25	0.231	157	0.1727	2631	NEUTRON DIFFRACTION	99
3.25-4.08	0.2007	138	0.17	2696	NEUTRON DIFFRACTION	99
4.08-14.6	0.1959	150	0.1738	2729	NEUTRON DIFFRACTION	96

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	2.66459368031	0.847660728068	-2.45625399914	4.80769376688	-0.279675188654	2.48251995493	0.230714670871	-0.19448010396	0.196685688761	0.10150942923	-0.0122597175491	0.0747753700235	-0.480309940844	0.0337435766554	-0.284483921419	0.112846704564	0.00881195421975	-0.0298994316273	0.182615337245	0.00911240021533	0.138979619098	25.0402871862	55.5300353471	84.8428776571
2	7.10587327634	3.784744542	-2.08260718574	3.12733452137	-1.22553756355	1.64496271227	0.0116782963941	0.0600721426143	0.0883264862107	0.130906271099	-0.10581306285	0.148772976844	0.0103500609267	-0.141656247468	0.102187726522	0.0928650612551	0.0172236802639	-0.0170948991337	0.127838194594	0.0253431011967	0.095720750218	18.683879818	52.1553199533	83.1315031631
3	0.314451981325	-0.80170691516	0.0373035245835	5.72487245944	4.32717918676	5.30937410421	-0.0757645478346	0.00209859343328	-0.0267882626633	-0.138772333943	0.101690158142	-0.24098986331	-0.270898383202	0.154792999402	-0.0599803614984	0.154390392391	-0.0379591261361	0.0138717104727	0.173727545773	0.0140896166057	0.192401131985	29.4647047084	61.18919944	76.1389086766
4	2.65163732726	-0.0333425526584	0.968501764472	3.8681731626	-0.697319431648	1.08161360803	0.00238780247616	0.0164131256336	0.145401646354	0.213974173073	-0.0542580534216	-0.0671295262621	-0.192643581135	0.039130318536	0.0279420364557	0.132891266971	-0.0211344569025	-0.0132393973462	0.129390979834	-0.00507815167392	0.122557146336	28.7756957047	58.390704358	86.0039848233
5	4.26320878438	3.71322000549	-1.93493841983	5.51172817502	-4.43674292232	6.59716108738	0.259025034248	-0.633089644056	0.213492827401	0.780657946109	-0.424051527966	-0.302326148297	-0.758025365343	0.404545793898	0.15192771992	0.24555148787	-0.0387760181786	-0.0632852736023	0.234301773956	-0.0380492537813	0.212781190176	34.0262336796	56.7120896486	96.542863961
6	3.09254674747	0.239276411813	0.088461553188	2.30589541385	0.45714626782	3.83531754348	0.0576226395093	-0.0849341670193	-0.0630276471277	0.2577881348	-0.0123790632959	-0.336302543714	0.00996708722733	0.27413414872	-0.0321998404564	0.147494829175	-0.0123599210736	-0.0378118119003	0.148730607591	0.0230774951469	0.167252219774	35.2981560224	46.3382385661	90.8758846431
7	8.04830801903	1.52515319322	4.87980995007	4.74737898356	1.21851349488	6.66141154062	0.218812894626	0.120004235455	-0.45557683006	0.0146730560815	-0.0049870058906	-0.661782325428	0.177136248801	0.616468218309	-0.175992862596	0.13138515452	0.0348975992227	0.00951280605671	0.155059779353	-0.00891399417107	0.247993874632	38.4142599531	37.5583991454	85.0020196211
8	4.22175811331	1.81694790264	-0.814678582351	4.05916342077	1.35250519378	7.29581373541	0.124338934413	-0.393817890247	-0.125279296318	0.36174359098	-0.0574382173681	0.0347248324488	0.406847912672	0.0670553825277	-0.0578129940528	0.126233206494	-0.0022602658407	-0.0192521409404	0.137559698885	0.0294893259495	0.154134618222	28.9697773803	40.5288350119	92.3491556399
9	4.15148508566	-0.427990444221	-1.41015521233	2.10960667155	1.14080073285	4.76729378879	-0.0265920008104	-0.0889818008937	-0.118252532892	0.17320275449	-0.068016822112	0.175488029421	0.137515225862	-0.329483327227	0.0715074275708	0.121690110168	-0.0245442113003	0.0036399865459	0.121461046994	0.0174240774832	0.110878940255	15.6559447763	41.4770835099	87.4939140096
10	5.82684858418	-2.63781411255	0.0588975371268	2.49608737407	1.48784859674	3.09034629448	0.00432886212607	-0.566654126069	-0.636697806311	0.407253622085	0.00102556703115	0.398172974073	0.897298851646	-0.521214989512	0.0169099025787	0.278816591017	-0.0986306662471	0.0235391445784	0.225910130259	0.0392686200177	0.238476982348	14.2721803133	33.9667568045	83.683373569
11	2.99593322131	-1.26160918088	-0.626479592968	2.59385084914	0.289678231268	2.24258251399	0.054058010465	0.0782296506581	0.169170200144	-0.198391557143	-0.0538857482381	0.02696686837	-0.205420549573	-0.0602435566619	-0.0166158574918	0.128022103873	-0.0201807489157	-0.0143591842757	0.114622126839	-0.0116522564697	0.1258307702	17.5312651187	54.8488853117	66.8110436751
12	3.3748241108	-0.442725672609	1.42129113766	5.38397829189	-0.320942374309	1.04956762145	-0.080747872889	0.338646617602	0.301792607191	-0.797234077381	-0.00254955535916	-0.019991103937	-0.53535263861	0.0246241513855	0.0875796441382	0.253310920432	-0.0349218518149	0.000655363363467	0.166260131027	0.048053287117	0.196768918351	17.5166135234	59.6458707264	58.135509926
13	2.68086267241	-3.46767763649	-2.4349077711	6.80384920886	0.528632763948	5.87489238463	-0.124532334711	-0.254662719063	0.143857187247	0.0878734205453	0.262733177674	0.430132023155	-0.231113906948	-0.293422799658	-0.0404609668646	0.124993733867	-0.00743314386485	-0.0489617968953	0.175103802703	-0.0139432181433	0.194409464255	6.19070437568	53.5553761432	65.2400492238
14	4.38814015536	-4.30398490602	-1.28015944335	6.38986502685	3.98472749135	3.81030490764	0.190216201682	0.617028142794	0.168260276395	-0.987624382511	-0.302886361164	0.407467156365	-0.413527703873	-0.387729647628	0.1046401879	0.321244295194	0.0138893150148	-0.0983936906893	0.227612766966	0.0508582625538	0.205078362944	6.892320028	53.7594225681	51.8877379389
15	4.04874102469	-0.281937126747	-0.73196065888	2.10949930493	0.0961530964746	3.22060384929	0.00863042632127	0.195436921631	0.0709111928483	-0.327979958551	0.00789841176544	0.306861255374	0.0148095556592	-0.407267905576	-0.0188610538874	0.192759111936	-0.0128977459907	-0.0563518999301	0.174131089822	-0.0044862301964	0.167439517726	4.86204595073	44.9104895546	58.9445344774
16	5.68756772417	-0.383779953294	4.78742465962	4.56070114865	-1.01678201036	7.31871932079	0.121716658869	-0.196815469524	-0.308503224186	-0.0936159508067	0.0290847189841	0.617852004626	0.263085312558	-0.788565084511	-0.126162482035	0.151464372159	-0.069364223504	-0.00851361848458	0.235319731939	0.0265839435284	0.206121954525	1.02105556634	37.0511015168	65.9557078442
17	3.56079509131	-1.39671032385	-0.680133745572	4.32255288464	2.69099632441	7.2249407596	0.08942256586	0.264704767787	-0.189352455697	-0.322327733889	-0.027078102849	0.0872503435391	0.417464612359	-0.277174128982	-0.0810734809172	0.149496496794	-0.0265796580472	-0.0336435556973	0.111623053671	-0.0141738359914	0.116656607942	10.7365384251	38.5746374877	58.4201583586
18	8.2525454638	-0.419843640447	-6.02020470985	2.61058150344	0.816481112477	7.87912254294	0.00699985711527	0.225057161331	0.00318195428046	-0.23882634275	0.0304007728848	-0.0838792648478	0.0713944292594	-0.035719042031	-0.030352068465	0.124593992856	-0.0036735538815	-0.0113297367969	0.118043712464	-0.00389113331434	0.111566190393	20.2801336557	40.7813206206	62.832645858
19	6.69268419726	-2.1196555077	4.29371349143	7.18136016786	-2.34891737501	3.12419536359	0.0616207291458	0.404373567544	-0.242351947092	-0.374590601433	-0.0439201777754	-0.231404184195	-0.0775371075594	0.924715042697	0.0109345623797	0.163394471127	-0.00274485018896	0.0540408136082	0.23176758048	-0.0187853282637	0.189141376372	30.2268182356	37.1520066468	63.6718040014
20	7.47640225237	2.70313449667	1.6748090222	3.92561727522	-1.58730863381	5.4892820343	0.0450666487791	0.388308307802	-0.538915890322	-0.281165686057	0.00718855104129	-0.237016897839	0.728852423261	0.216410107741	-0.0234547495615	0.204180920667	0.0383521370042	0.0104151233286	0.129462103967	-0.0232317272634	0.182550914616	25.1662505228	32.1961271599	68.3117739795

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 'B' and (resid 2 through 14 )	B	C	2 - 14	1 - 13
2	2	chain 'B' and (resid 15 through 36 )	B	C	15 - 36	14 - 35
3	3	chain 'B' and (resid 37 through 51 )	B	C	37 - 51	36 - 50
4	4	chain 'B' and (resid 52 through 85 )	B	C	52 - 85	51 - 84
5	5	chain 'B' and (resid 86 through 97 )	B	C	86 - 97	85 - 96
6	6	chain 'B' and (resid 98 through 127 )	B	C	98 - 127	97 - 126
7	7	chain 'B' and (resid 128 through 143 )	B	C	128 - 143	127 - 142
8	8	chain 'B' and (resid 144 through 157 )	B	C	144 - 157	143 - 156
9	9	chain 'B' and (resid 158 through 184 )	B	C	158 - 184	157 - 183
10	10	chain 'B' and (resid 185 through 196 )	B	C	185 - 196	184 - 195
11	11	chain 'A' and (resid 2 through 51 )	A	A	2 - 51	1 - 50
12	12	chain 'A' and (resid 52 through 68 )	A	A	52 - 68	51 - 67
13	13	chain 'A' and (resid 69 through 85 )	A	A	69 - 85	68 - 84
14	14	chain 'A' and (resid 86 through 97 )	A	A	86 - 97	85 - 96
15	15	chain 'A' and (resid 98 through 127 )	A	A	98 - 127	97 - 126
16	16	chain 'A' and (resid 128 through 143 )	A	A	128 - 143	127 - 142
17	17	chain 'A' and (resid 144 through 157 )	A	A	144 - 157	143 - 156
18	18	chain 'A' and (resid 158 through 173 )	A	A	158 - 173	157 - 172
19	19	chain 'A' and (resid 174 through 184 )	A	A	174 - 184	173 - 183
20	20	chain 'A' and (resid 185 through 196 )	A	A	185 - 196	184 - 195

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