PDB-4wh0: YcaC from Pseudomonas aeruginosa with S-mercaptocysteine active s...

ID or keywords:

Entry

Database: PDB / ID: 4wh0

Title

YcaC from Pseudomonas aeruginosa with S-mercaptocysteine active site cysteine

Components

Putative 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: 2.563 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 19, 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 ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.2	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4wh0.cif.gz	749.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4wh0.ent.gz	517.3 KB	Display	PDB format
PDBx/mmJSON format	4wh0.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/wh/4wh0 ftp://data.pdbj.org/pub/pdb/validation_reports/wh/4wh0	HTTPS FTP

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Related structure data

Related structure data	4wgfC 1yacS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4wgf-d 4zde-1 6p2t-1 2dub-d 4zdf-1 5cgz-2 7lox-1 1pjh-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: Putative hydrolase

B: Putative hydrolase

C: Putative hydrolase

D: Putative hydrolase

E: Putative hydrolase

F: Putative hydrolase

G: Putative hydrolase

H: Putative hydrolase

hetero molecules

182 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)	74.46, 114.53, 96.16
Angle α, β, γ (deg.)	90.0, 91.9, 90.0
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

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	1	SER	SER	THR	THR	chain 'A'	A	A	2 - 58	2 - 58
1	2	PHE	PHE	GLU	GLU	chain 'A'	A	A	60 - 74	60 - 74
1	3	PHE	PHE	VAL	VAL	chain 'A'	A	A	76 - 117	76 - 117
1	4	VAL	VAL	ARG	ARG	chain 'A'	A	A	119 - 154	119 - 154
1	5	THR	THR	LEU	LEU	chain 'A'	A	A	156 - 162	156 - 162
1	6	ASN	ASN	THR	THR	chain 'A'	A	A	164 - 203	164 - 203
2	7	SER	SER	THR	THR	chain 'B'	B	B	2 - 58	2 - 58
2	8	PHE	PHE	GLU	GLU	chain 'B'	B	B	60 - 74	60 - 74
2	9	PHE	PHE	VAL	VAL	chain 'B'	B	B	76 - 117	76 - 117
2	10	VAL	VAL	ARG	ARG	chain 'B'	B	B	119 - 154	119 - 154
2	11	THR	THR	LEU	LEU	chain 'B'	B	B	156 - 162	156 - 162
2	12	ASN	ASN	THR	THR	chain 'B'	B	B	164 - 203	164 - 203
3	13	SER	SER	THR	THR	chain 'C'	C	C	2 - 58	2 - 58
3	14	PHE	PHE	GLU	GLU	chain 'C'	C	C	60 - 74	60 - 74
3	15	PHE	PHE	VAL	VAL	chain 'C'	C	C	76 - 117	76 - 117
3	16	VAL	VAL	ARG	ARG	chain 'C'	C	C	119 - 154	119 - 154
3	17	THR	THR	LEU	LEU	chain 'C'	C	C	156 - 162	156 - 162
3	18	ASN	ASN	THR	THR	chain 'C'	C	C	164 - 203	164 - 203
4	19	SER	SER	THR	THR	chain 'D'	D	D	2 - 58	2 - 58
4	20	PHE	PHE	GLU	GLU	chain 'D'	D	D	60 - 74	60 - 74
4	21	PHE	PHE	VAL	VAL	chain 'D'	D	D	76 - 117	76 - 117
4	22	VAL	VAL	ARG	ARG	chain 'D'	D	D	119 - 154	119 - 154
4	23	THR	THR	LEU	LEU	chain 'D'	D	D	156 - 162	156 - 162
4	24	ASN	ASN	THR	THR	chain 'D'	D	D	164 - 203	164 - 203
5	25	SER	SER	THR	THR	chain 'E'	E	E	2 - 58	2 - 58
5	26	PHE	PHE	GLU	GLU	chain 'E'	E	E	60 - 74	60 - 74
5	27	PHE	PHE	VAL	VAL	chain 'E'	E	E	76 - 117	76 - 117
5	28	VAL	VAL	ARG	ARG	chain 'E'	E	E	119 - 154	119 - 154
5	29	THR	THR	LEU	LEU	chain 'E'	E	E	156 - 162	156 - 162
5	30	ASN	ASN	THR	THR	chain 'E'	E	E	164 - 203	164 - 203
6	31	SER	SER	THR	THR	chain 'F'	F	F	2 - 58	2 - 58
6	32	PHE	PHE	GLU	GLU	chain 'F'	F	F	60 - 74	60 - 74
6	33	PHE	PHE	VAL	VAL	chain 'F'	F	F	76 - 117	76 - 117
6	34	VAL	VAL	ARG	ARG	chain 'F'	F	F	119 - 154	119 - 154
6	35	THR	THR	LEU	LEU	chain 'F'	F	F	156 - 162	156 - 162
6	36	ASN	ASN	THR	THR	chain 'F'	F	F	164 - 203	164 - 203
7	37	SER	SER	THR	THR	chain 'G'	G	G	2 - 58	2 - 58
7	38	PHE	PHE	GLU	GLU	chain 'G'	G	G	60 - 74	60 - 74
7	39	PHE	PHE	VAL	VAL	chain 'G'	G	G	76 - 117	76 - 117
7	40	VAL	VAL	ARG	ARG	chain 'G'	G	G	119 - 154	119 - 154
7	41	THR	THR	LEU	LEU	chain 'G'	G	G	156 - 162	156 - 162
7	42	ASN	ASN	THR	THR	chain 'G'	G	G	164 - 203	164 - 203
8	43	SER	SER	THR	THR	chain 'H'	H	H	2 - 58	2 - 58
8	44	PHE	PHE	GLU	GLU	chain 'H'	H	H	60 - 74	60 - 74
8	45	PHE	PHE	VAL	VAL	chain 'H'	H	H	76 - 117	76 - 117
8	46	VAL	VAL	ARG	ARG	chain 'H'	H	H	119 - 154	119 - 154
8	47	THR	THR	LEU	LEU	chain 'H'	H	H	156 - 162	156 - 162
8	48	ASN	ASN	THR	THR	chain 'H'	H	H	164 - 203	164 - 203

#1: Protein	Putative hydrolase Mass: 22712.211 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: Q02J38, UniProt: Q9I4D6*PLUS
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.51 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.75 Details: 20% PEG 3350, 200 mM Na malonate, and 100 mM MES-NaOH ph 6.75.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9686 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 5, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9686 Å / Relative weight: 1
Reflection	Resolution: 2.563→48.05 Å / Num. obs: 47067 / % possible obs: 91 % / Redundancy: 8.2 % / Net I/σ(I): 11.32
Reflection shell	Resolution: 2.563→2.655 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.62 / % possible all: 58

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1YAC

1yac

Resolution: 2.563→48.05 Å / SU ML: 0.281259156635 / Cross valid method: FREE R-VALUE / σ(F): 1.35322504183 / Phase error: 19.9624891103 / Stereochemistry target values: GeoStd + Monomer Library

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.191040385402	2383	5.06331803502 %	Random selection
R_work	0.145722396373	44681	-	-
obs	0.148073307849	47064	90.7625255525 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 27.9352165414 Å²

Refinement step

Cycle: LAST / Resolution: 2.563→48.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12496	0	8	423	12927

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00371649518601	12916
X-RAY DIFFRACTION	f_angle_d	0.822144906247	17617
X-RAY DIFFRACTION	f_chiral_restr	0.0360626142305	1955
X-RAY DIFFRACTION	f_plane_restr	0.00355736404356	2327
X-RAY DIFFRACTION	f_dihedral_angle_d	11.221476079	4521

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 (%)
2.5626-2.6149	0.26600761046	88	0.228062012598	1611	X-RAY DIFFRACTION	55.9065482066
2.6149-2.6718	0.295711384832	77	0.214462071337	1824	X-RAY DIFFRACTION	61.9218241042
2.6718-2.7339	0.285103380431	98	0.208602959888	1955	X-RAY DIFFRACTION	68.0026498841
2.7339-2.8023	0.258174112967	119	0.202243946875	2145	X-RAY DIFFRACTION	75.2909876954
2.8023-2.878	0.251495959795	133	0.20750645812	2445	X-RAY DIFFRACTION	85.1105975569
2.878-2.9627	0.253088102762	151	0.191501922741	2827	X-RAY DIFFRACTION	97.6073418551
2.9627-3.0583	0.244096666209	158	0.190749353568	2873	X-RAY DIFFRACTION	99.9340586878
3.0583-3.1676	0.235677156889	143	0.175592305438	2909	X-RAY DIFFRACTION	99.9672453325
3.1676-3.2944	0.225103212661	154	0.167995151235	2872	X-RAY DIFFRACTION	99.9669639907
3.2944-3.4443	0.22479457177	171	0.160362815901	2881	X-RAY DIFFRACTION	99.9345121153
3.4443-3.6258	0.183139300288	155	0.129342941572	2878	X-RAY DIFFRACTION	100
3.6258-3.8529	0.159204450098	160	0.118808117707	2902	X-RAY DIFFRACTION	99.967352269
3.8529-4.1503	0.16197052143	176	0.117548526681	2894	X-RAY DIFFRACTION	100
4.1503-4.5677	0.135778237805	154	0.103678184717	2893	X-RAY DIFFRACTION	99.967191601
4.5677-5.228	0.159077805657	154	0.108666604098	2891	X-RAY DIFFRACTION	99.9343616672
5.228-6.5842	0.155676616731	144	0.132534427236	2929	X-RAY DIFFRACTION	100
6.5842-49.2033	0.14743100822	148	0.124729607075	2952	X-RAY DIFFRACTION	98.9151244416

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	0.741916009644	0.112689400217	0.16864683539	1.2085476059	-0.150087699988	0.737274289213	-0.0251070562616	-0.0244257539949	-0.0066635553012	0.077890686035	0.0327659446483	0.0101134640864	-0.0592650346519	-0.0766480502461	0.0152033302398	0.131675418604	-0.00808886131062	0.00877734605208	0.160488017507	-0.011898857597	0.127113209901	32.4980633093	19.8311983642	35.7448293616
2	0.647848386397	0.0214139637436	-0.363170364294	1.04358083249	-0.0941211813186	0.992505034124	1.47838736778E-5	0.0468878050556	0.0440371862534	-0.217746360977	-0.0353189737178	0.0497297325468	0.019446204481	0.0212654721847	0.0272805096592	0.180803979458	-0.0219685839135	-0.0156483409068	0.201350018123	0.0232205221274	0.118131460886	32.5556016589	13.7312436771	5.69894753137
3	0.774511718028	-0.25721556931	0.099567203575	0.981005630079	-0.0729436773751	0.713738681444	-0.0114182391324	0.0715018882643	0.0145607734951	-0.177576947329	0.0107290155761	-0.055910756952	0.0607425342749	-0.00318924320984	-0.00298282453388	0.189926015129	-0.00136710046062	0.0186431508382	0.178626371713	-0.0169042053419	0.13326713827	37.3807607478	-15.9197397667	11.7007267371
4	0.88471858505	0.0732246148173	0.459980577822	1.2867534808	0.163394770781	0.891940199946	0.00326457713148	0.0406757603523	-0.048994333352	0.107896912946	0.00335187404459	-0.0235465609045	-0.0151004145241	0.0354846605273	-0.00511711662928	0.130179604983	0.00475092897388	0.0217730117953	0.15977315663	0.0135500431358	0.104368857386	37.1839786394	-9.87694828456	41.803981388
5	0.748105745583	0.0608231034399	-0.698095911387	0.883311401614	-0.259730817177	0.736900755869	-0.00144125951547	0.0268758693996	0.0809673329915	0.174349536453	-0.00744095048503	0.18827015928	-0.0473465267123	0.0213286321441	-0.00460100585501	0.152545854709	-0.0071336456303	0.0240402339097	0.18383895247	-0.00199405889736	0.217580306035	0.0664387704218	8.98940046485	42.3958370157
6	0.603917792033	0.118153187816	-0.0102822970393	1.0384993836	0.385596786044	0.998976268576	-0.0340476961434	0.00630726902146	-0.0769010834175	0.0964771193274	0.0290530236144	0.190761455707	0.0981762120845	-0.00921513389133	0.00339432789804	0.149468752983	-0.00329025236538	0.0235865879835	0.184869709923	0.03804313252	0.271701077296	4.62230037102	-20.9129057858	36.7975268698
7	0.892431918013	-0.0958210592577	0.27484144166	1.17198310702	0.107774878359	0.53099929262	0.00493133227295	0.140753168403	-0.131981690234	-0.302642697451	0.0267357216354	0.242821852907	0.0918888660567	-0.0357522555521	-0.0317223211948	0.256464225924	-0.0251881855278	-0.0836270194928	0.211579879116	-0.00863376547156	0.246736797897	2.87839948858	-15.4280043137	6.79907576096
8	1.01373864034	-0.113989187718	-0.0231255145861	0.867959358492	0.152116809091	1.28415047157	0.0377573227484	0.0712635528028	0.0379475347334	-0.157399554138	0.0414602283727	0.251547763935	-0.0766707218014	-0.0102123723698	-0.0788807290065	0.190199479287	-0.0100749120214	-0.0558168419122	0.180301039585	0.0567562797091	0.284246651755	-1.4830304793	14.5153720219	12.3662563627

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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