PDB-4wgf: YcaC from Pseudomonas aeruginosa with hexane-2,5-diol and covalen...

ID or keywords:

Entry

Database: PDB / ID: 4wgf

Title

YcaC from Pseudomonas aeruginosa with hexane-2,5-diol and covalent acrylamide

Components

Probable hydrolase

Keywords

HYDROLASE / Co-purified / parallel beta-sheet / contaminant.

Function / homology

Function and homology information

hydrolase activity
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.34020690848 Å

Authors

Groftehauge, M.K. / Truan, D. / Vasil, A. / Denny, P.W. / Vasil, M.L. / Pohl, E.

Funding support

United Kingdom, 1items

Citation

Journal: Int J Mol Sci / Year: 2015
Title: Crystal Structure of a Hidden Protein, YcaC, a Putative Cysteine Hydrolase from Pseudomonas aeruginosa, with and without an Acrylamide Adduct.
Authors: Grftehauge, M.K. / Truan, D. / Vasil, A. / Denny, P.W. / Vasil, M.L. / Pohl, E.

History

Deposition	Sep 18, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jul 29, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jan 10, 2024	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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4wgf.cif.gz	761.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4wgf.ent.gz	522.4 KB	Display	PDB format
PDBx/mmJSON format	4wgf.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/4wgf ftp://data.pdbj.org/pub/pdb/validation_reports/wg/4wgf	HTTPS FTP

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Related structure data

Related structure data	4wh0C 1yacS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4wh0-d 4zdf-1 1yac-1 5cgz-2 4zde-1 1pjh-1 5cgz-1 6ull-1 Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: Probable hydrolase

B: Probable hydrolase

C: Probable hydrolase

D: Probable hydrolase

E: Probable hydrolase

F: Probable hydrolase

G: Probable hydrolase

H: Probable hydrolase

hetero molecules

184 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	158.36, 74.48, 141.06
Angle α, β, γ (deg.)	90.0, 92.29, 90.0
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1
5	1
6	1
7	1
8	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	2	SER	SER	GLU	GLU	chain 'A'	A	A	2 - 74	2 - 74
1	3	PHE	PHE	ARG	ARG	chain 'A'	A	A	76 - 154	76 - 154
1	4	THR	THR	LEU	LEU	chain 'A'	A	A	156 - 162	156 - 162
1	5	ASN	ASN	THR	THR	chain 'A'	A	A	164 - 203	164 - 203
2	6	SER	SER	GLU	GLU	chain 'B'	B	B	2 - 74	2 - 74
2	7	PHE	PHE	ARG	ARG	chain 'B'	B	B	76 - 154	76 - 154
2	8	THR	THR	LEU	LEU	chain 'B'	B	B	156 - 162	156 - 162
2	9	ASN	ASN	THR	THR	chain 'B'	B	B	164 - 203	164 - 203
3	10	SER	SER	GLU	GLU	chain 'C'	C	C	2 - 74	2 - 74
3	11	PHE	PHE	ARG	ARG	chain 'C'	C	C	76 - 154	76 - 154
3	12	THR	THR	LEU	LEU	chain 'C'	C	C	156 - 162	156 - 162
3	13	ASN	ASN	THR	THR	chain 'C'	C	C	164 - 203	164 - 203
4	14	SER	SER	GLU	GLU	chain 'D'	D	D	2 - 74	2 - 74
4	15	PHE	PHE	ARG	ARG	chain 'D'	D	D	76 - 154	76 - 154
4	16	THR	THR	LEU	LEU	chain 'D'	D	D	156 - 162	156 - 162
4	17	ASN	ASN	THR	THR	chain 'D'	D	D	164 - 203	164 - 203
5	18	SER	SER	GLU	GLU	chain 'E'	E	E	2 - 74	2 - 74
5	19	PHE	PHE	ARG	ARG	chain 'E'	E	E	76 - 154	76 - 154
5	20	THR	THR	LEU	LEU	chain 'E'	E	E	156 - 162	156 - 162
5	21	ASN	ASN	THR	THR	chain 'E'	E	E	164 - 203	164 - 203
6	22	SER	SER	GLU	GLU	chain 'F'	F	F	2 - 74	2 - 74
6	23	PHE	PHE	ARG	ARG	chain 'F'	F	F	76 - 154	76 - 154
6	24	THR	THR	LEU	LEU	chain 'F'	F	F	156 - 162	156 - 162
6	25	ASN	ASN	THR	THR	chain 'F'	F	F	164 - 203	164 - 203
7	26	SER	SER	GLU	GLU	chain 'G'	G	G	2 - 74	2 - 74
7	27	PHE	PHE	ARG	ARG	chain 'G'	G	G	76 - 154	76 - 154
7	28	THR	THR	LEU	LEU	chain 'G'	G	G	156 - 162	156 - 162
7	29	ASN	ASN	THR	THR	chain 'G'	G	G	164 - 203	164 - 203
8	30	SER	SER	GLU	GLU	chain 'H'	H	H	2 - 74	2 - 74
8	31	PHE	PHE	ARG	ARG	chain 'H'	H	H	76 - 154	76 - 154
8	32	THR	THR	LEU	LEU	chain 'H'	H	H	156 - 162	156 - 162
8	33	ASN	ASN	THR	THR	chain 'H'	H	H	164 - 203	164 - 203

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein	Probable hydrolase Mass: 22680.146 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / Variant: PADD1976 / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / References: UniProt: Q9I4D6

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Non-polymers , 5 types, 1092 molecules

#2: Chemical	ChemComp-ROP / PROPIONAMIDE / Propanamide Mass: 73.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₇NO
#3: Chemical	ChemComp-HX2 / (2R,5R)-hexane-2,5-diol Mass: 118.174 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₆H₁₄O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1059 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.34 % / Description: Extremely thin, single needle crystals.
Crystal grow	Temperature: 292 K / Method: vapor diffusion / pH: 6.75 Details: Crystal produced from streak seeding. Mother liquor: 26% w/v PEG 3350, 400 mM (NH4)2SO4, and 70 mM BisTris-HCl pH 6.75. Protein buffer: 50 mM NaCl, 50 mM Tris-HCl pH 7.4, 4% 1-,4-dioxane, and 0.1 mM TCEP.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9537 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 16, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.34→31.72 Å / Num. obs: 60390 / % possible obs: 87 % / Redundancy: 4 % / B_iso Wilson estimate: 12.18 Å² / R_merge(I) obs: 0.1559 / Net I/σ(I): 11.68
Reflection shell	Resolution: 2.34→2.424 Å / Redundancy: 1.3 % / R_merge(I) obs: 0.276 / Mean I/σ(I) obs: 4.59 / % possible all: 36

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Processing

Software

Name	Version	Classification
XDS		data reduction
PHENIX	dev_1745	refinement
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1YAC

1yac

Resolution: 2.34020690848→31.72 Å / SU ML: 0.241301768967 / Cross valid method: FREE R-VALUE / σ(F): 1.33592006581 / Phase error: 19.8919583698 / Stereochemistry target values: GeoStd + Monomer Library

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.203845887682	3058	5.06744440394 %	Random selection
R_work	0.172182821447	57288	-	-
obs	0.173799820715	60346	86.8025488701 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 14.9697430435 Å²

Refinement step

Cycle: LAST / Resolution: 2.34020690848→31.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12488	0	157	1059	13704

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0023316997053	12998
X-RAY DIFFRACTION	f_angle_d	0.670963407373	17693
X-RAY DIFFRACTION	f_chiral_restr	0.0278780703328	1966
X-RAY DIFFRACTION	f_plane_restr	0.00266053029077	2322
X-RAY DIFFRACTION	f_dihedral_angle_d	11.1788438853	4531

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 (%)
2.3402-2.3768	0.269107571697	47	0.23060307075	867	X-RAY DIFFRACTION	29.1082802548
2.3768-2.4157	0.239423535587	65	0.224769901858	1244	X-RAY DIFFRACTION	41.7543859649
2.4157-2.4574	0.302051241983	69	0.214409856501	1352	X-RAY DIFFRACTION	45.5011207173
2.4574-2.5021	0.246465487441	105	0.20594934807	1803	X-RAY DIFFRACTION	60.2462898642
2.5021-2.5502	0.26444586045	124	0.217961468677	2184	X-RAY DIFFRACTION	73.9980763065
2.5502-2.6022	0.264142818265	129	0.218187556589	2458	X-RAY DIFFRACTION	82.9166666667
2.6022-2.6588	0.252731139701	145	0.208518049415	2693	X-RAY DIFFRACTION	88.9934148636
2.6588-2.7206	0.2692929862	143	0.207038379696	2724	X-RAY DIFFRACTION	91.8027537624
2.7206-2.7886	0.258119210237	156	0.201169888619	2895	X-RAY DIFFRACTION	97.819814043
2.7886-2.864	0.27011655772	150	0.208660248164	2996	X-RAY DIFFRACTION	98.6825595985
2.864-2.9482	0.234545613898	144	0.194543606809	2951	X-RAY DIFFRACTION	99.7421849823
2.9482-3.0434	0.249374458409	157	0.202536526198	3000	X-RAY DIFFRACTION	99.8734577665
3.0434-3.1521	0.215356312191	164	0.181827277934	2990	X-RAY DIFFRACTION	99.9683042789
3.1521-3.2782	0.218612780276	162	0.180849200571	2986	X-RAY DIFFRACTION	99.8097653773
3.2782-3.4273	0.190852401438	154	0.17625720535	3006	X-RAY DIFFRACTION	99.9683644416
3.4273-3.6079	0.186789514117	180	0.159954917937	2984	X-RAY DIFFRACTION	99.7163567602
3.6079-3.8338	0.184213651014	154	0.142631001223	2996	X-RAY DIFFRACTION	99.9365482234
3.8338-4.1295	0.176957323536	158	0.144838614245	3006	X-RAY DIFFRACTION	99.9052731291
4.1295-4.5444	0.150378558574	170	0.126814680484	3004	X-RAY DIFFRACTION	99.779943414
4.5444-5.2006	0.136001832057	168	0.129692430661	2998	X-RAY DIFFRACTION	99.8738170347
5.2006-6.5469	0.160507544177	172	0.159224910751	3039	X-RAY DIFFRACTION	99.9377528789
6.5469-38.2413	0.156010488969	142	0.145957320072	3112	X-RAY DIFFRACTION	98.6658580958

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	0.589709488031	-0.231002273302	0.237482751271	0.431041668328	-0.0839238914761	0.441455050481	0.0557053826941	0.00290400142652	-0.0172595346543	0.0224503715479	-0.00485059438228	0.094581328404	0.00389401235735	-0.0814080853445	-0.038834852789	0.0693508775661	-0.000385333273323	0.0117738605083	0.0866394293792	0.000344115742894	0.10754528934	-77.5419464442	23.350798822	38.3119026906
2	0.786213702798	0.149464520088	-0.235283810618	0.757179953974	-0.156846975332	0.526093697557	-0.00548838352231	0.161207054174	-0.0114117886452	-0.023528694314	0.0311942751822	0.0242905481172	-0.0594301758189	-0.0439718665017	-0.0199259911182	0.103126937294	0.0169986309343	-0.018104429407	0.0954036943356	0.00130498332341	0.055096531686	-60.7625305549	24.0237538259	12.8300958304
3	0.561668712563	0.113092300952	0.0975665946802	0.697632565714	0.105461142318	0.781276139453	0.0192046834142	0.0072044994427	0.0326584233174	0.0141754150235	-0.00939643514412	-0.0171206057877	-0.0557522268225	0.084615832967	-0.0135165483014	0.0659078856308	0.00134216110887	0.0142867139064	0.0922310151465	0.00767607379421	0.100334013897	-35.5671624209	28.8427430703	29.4264755814
4	0.837049324431	-0.0381614538268	-0.130662781434	0.460046100476	0.113276960264	0.68341038904	0.0410733344148	-0.0811298522328	0.0692797274507	0.0605695075848	-0.027409718877	0.0228243961056	-0.0143441555732	-0.00222713578365	0.0021315875645	0.11155154008	-0.00878985096357	-0.00274153642602	0.0782478330414	-0.0130718610728	0.054621175016	-52.3705455101	27.9330548061	55.0339751643
5	0.451440611227	0.197179065447	-0.0251843725624	0.492580334784	-0.238931391562	0.892608129389	0.0185728616533	-0.0816457043207	-0.0506333299879	0.0491490470971	-0.0227480255375	0.0648764391584	0.0282015171103	-0.0697565175559	0.0040187763646	0.0866088399613	-0.00902359455987	0.0105639611863	0.0815684085478	0.00298146682296	0.112770534629	-69.8537785343	-9.08170748494	47.9462146362
6	0.850382418198	-0.178392931304	0.08756556722	0.539901969938	-0.0874215992073	0.488833437544	-0.0114735047256	-0.0546327422573	0.00441635774779	0.059415623132	-0.007989035232	-0.0439047385049	0.0396957176225	0.0841412399573	0.0255542983354	0.0938935261027	-0.00247548009871	0.00605164791897	0.0761425205338	0.0063485142063	0.0639417033602	-40.1947046804	-4.3959708213	54.0994156563
7	0.488998617409	0.0404644074139	0.123482473324	0.618010117732	0.19377256573	0.531415562394	0.000929683721159	0.0564488213833	-0.0477455794316	0.00812119959008	0.0233568993697	-0.0637300309562	0.0656719329853	0.0725710512874	-0.0186175997484	0.0698839871832	0.0176965285958	0.00359592623062	0.0858105045652	0.00129984103832	0.0782662487005	-33.9102219786	-5.55124458502	24.238671317
8	0.459964333396	0.258518000029	-0.0708412725983	0.57121248552	-0.163961473263	0.496027193785	0.0105796471641	0.0547823356893	-0.0539469287127	-0.0290812417378	-0.00749915270213	0.0530185922694	0.0486606611637	-0.0782697057423	0.00301453858293	0.0987923699707	0.000827619839702	-0.0120751225137	0.0858577018566	-0.0141330759737	0.104324597632	-63.5137846314	-10.1923706834	17.999655345

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'A' and resid 2 through 203)
2	X-RAY DIFFRACTION	2	(chain 'B' and resid 2 through 203)
3	X-RAY DIFFRACTION	3	(chain 'C' and resid 2 through 203)
4	X-RAY DIFFRACTION	4	(chain 'D' and resid 2 through 203)
5	X-RAY DIFFRACTION	5	(chain 'E' and resid 2 through 203)
6	X-RAY DIFFRACTION	6	(chain 'F' and resid 2 through 203)
7	X-RAY DIFFRACTION	7	(chain 'G' and resid 2 through 203)
8	X-RAY DIFFRACTION	8	(chain 'H' and resid 2 through 203)

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Protein , 1 types, 8 molecules ABCDEFGH

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Non-polymers , 5 types, 1092 molecules

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-Non-polymers , 5 types, 1092 molecules

-Experimental details

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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

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Related structure data

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Links

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Assembly

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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Non-polymers , 5 types, 1092 molecules

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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

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About Yorodumi

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Yorodumi