PDB-4wjb: X-ray crystal structure of a putative amidohydrolase/peptidase fr...

ID or keywords:

Entry

Database: PDB / ID: 4wjb

Title

X-ray crystal structure of a putative amidohydrolase/peptidase from Burkholderia cenocepacia

Components

Putative amidohydrolase/peptidase

Keywords

HYDROLASE / infectious disease / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines / metal ion binding
Similarity search - Function

Biological species

Burkholderia cenocepacia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Lukacs, C.M. / Dranow, D.M. / Edwards, T.E. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To Be Published
Title: X-ray crystal structure of a putative amidohydrolase/peptidase from Burkholderia cenocepacia
Authors: Lukacs, C.M. / Dranow, D.M. / Edwards, T.E. / Lorimer, D.

History

Deposition	Sep 29, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 8, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_conn / struct_keywords Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_keywords.text

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4wjb.cif.gz	636.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4wjb.ent.gz	527.3 KB	Display	PDB format
PDBx/mmJSON format	4wjb.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4wjb_validation.pdf.gz	479 KB	Display	wwPDB validaton report
Full document	4wjb_full_validation.pdf.gz	483.9 KB	Display
Data in XML	4wjb_validation.xml.gz	66.3 KB	Display
Data in CIF	4wjb_validation.cif.gz	97.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wj/4wjb ftp://data.pdbj.org/pub/pdb/validation_reports/wj/4wjb	HTTPS FTP

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Related structure data

Related structure data	1r3nS S: Starting model for refinement
Similar structure data	2imo-d 1r1l-d 4o23-d 2v8v-2 4pqa-1 1oyh-d 2v8v-1 2pok-d 3in9-2 2b4x-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: BuceA.12245.b

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (5)

Deposited unit

A: Putative amidohydrolase/peptidase

B: Putative amidohydrolase/peptidase

C: Putative amidohydrolase/peptidase

D: Putative amidohydrolase/peptidase

hetero molecules

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

1

A: Putative amidohydrolase/peptidase

D: Putative amidohydrolase/peptidase

hetero molecules

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

2

B: Putative amidohydrolase/peptidase

C: Putative amidohydrolase/peptidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	64.660, 113.060, 126.670
Angle α, β, γ (deg.)	90.00, 95.50, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Putative amidohydrolase/peptidase Mass: 45536.191 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia (bacteria) Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610 Gene: BCAM1221 / Production host: Escherichia coli (E. coli) References: UniProt: B4EHA1, N-carbamoyl-L-amino-acid hydrolase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1190 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.39 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: JCSG+h7: 25% PEG3350, 02M ammonium sulfate, 0.1M Bis Tris pH5.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Aug 13, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9787 Å / Relative weight: 1
Reflection	Resolution: 1.95→8.72 Å / Num. obs: 131228 / % possible obs: 99.5 % / Redundancy: 3.2 % / R_merge(I) obs: 0.074 / Net I/σ(I): 12.4
Reflection shell	Resolution: 1.95→2 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.517 / % possible all: 99.8

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Processing

Software

Name: PHENIX / Version: (phenix.refine: dev_1779) / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1R3N

1r3n

Resolution: 1.95→8.72 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.78 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2132	6462	4.93 %
R_work	0.173	-	-
obs	0.1749	131173	99.53 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→8.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12190	0	87	1190	13467

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.019	12605
X-RAY DIFFRACTION	f_angle_d	0.841	17091
X-RAY DIFFRACTION	f_dihedral_angle_d	12.307	4515
X-RAY DIFFRACTION	f_chiral_restr	0.033	1893
X-RAY DIFFRACTION	f_plane_restr	0.004	2290

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 (%)
1.95-1.9722	0.2822	232	0.243	4110	X-RAY DIFFRACTION	100
1.9722-1.9954	0.3028	193	0.2328	4135	X-RAY DIFFRACTION	100
1.9954-2.0197	0.2699	243	0.2278	4194	X-RAY DIFFRACTION	100
2.0197-2.0453	0.2789	216	0.221	4119	X-RAY DIFFRACTION	100
2.0453-2.0722	0.2558	186	0.2078	4121	X-RAY DIFFRACTION	99
2.0722-2.1006	0.2658	217	0.2061	4170	X-RAY DIFFRACTION	100
2.1006-2.1306	0.2592	196	0.1967	4139	X-RAY DIFFRACTION	100
2.1306-2.1624	0.2223	221	0.1906	4204	X-RAY DIFFRACTION	100
2.1624-2.1962	0.2386	205	0.1865	4104	X-RAY DIFFRACTION	100
2.1962-2.2322	0.2553	186	0.1895	4242	X-RAY DIFFRACTION	100
2.2322-2.2707	0.2394	212	0.1855	4114	X-RAY DIFFRACTION	99
2.2707-2.312	0.2192	232	0.1808	4150	X-RAY DIFFRACTION	100
2.312-2.3564	0.193	192	0.1745	4185	X-RAY DIFFRACTION	100
2.3564-2.4045	0.2254	201	0.1731	4178	X-RAY DIFFRACTION	100
2.4045-2.4568	0.2333	237	0.1768	4149	X-RAY DIFFRACTION	100
2.4568-2.514	0.2309	244	0.1763	4100	X-RAY DIFFRACTION	100
2.514-2.5768	0.2439	213	0.1789	4181	X-RAY DIFFRACTION	100
2.5768-2.6465	0.2287	209	0.1777	4179	X-RAY DIFFRACTION	100
2.6465-2.7244	0.2253	234	0.1738	4132	X-RAY DIFFRACTION	100
2.7244-2.8123	0.2232	233	0.1774	4190	X-RAY DIFFRACTION	100
2.8123-2.9128	0.2405	203	0.1703	4148	X-RAY DIFFRACTION	100
2.9128-3.0294	0.2078	217	0.1738	4161	X-RAY DIFFRACTION	100
3.0294-3.1672	0.2332	217	0.1814	4150	X-RAY DIFFRACTION	99
3.1672-3.3342	0.2344	227	0.1759	4157	X-RAY DIFFRACTION	99
3.3342-3.543	0.1962	205	0.1672	4148	X-RAY DIFFRACTION	99
3.543-3.8165	0.2094	222	0.1607	4185	X-RAY DIFFRACTION	99
3.8165-4.2003	0.1635	216	0.1486	4146	X-RAY DIFFRACTION	99
4.2003-4.8076	0.1617	213	0.1354	4143	X-RAY DIFFRACTION	99
4.8076-6.0551	0.1815	225	0.1564	4175	X-RAY DIFFRACTION	99
6.0551-47.3787	0.165	215	0.1612	4202	X-RAY DIFFRACTION	98

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	2.0554	0.1084	0.0162	0.7018	-0.3765	1.9689	0.0858	-0.0839	-0.0161	-0.038	-0.0042	-0.0047	0.0865	0.15	-0.089	0.1295	-0.0043	-0.0037	0.0892	-0.0165	0.1879	-105.03	157.1666	262.46
2	2.2837	-0.0402	-1.6192	0.9565	0.3628	1.7432	0.2399	0.2072	0.2468	-0.1255	-0.1364	0.0335	-0.2851	-0.1691	-0.1234	0.2198	0.0091	0.0106	0.1584	-0.0167	0.2076	-82.8585	170.8175	240.5105
3	3.0095	0.4196	1.1325	1.697	-1.8619	2.9823	0.1829	-0.135	0.0462	-0.0232	-0.1368	-0.0899	0.0538	0.3673	-0.0426	0.1559	-0.0353	0.0218	0.233	-0.0694	0.1782	-94.8968	163.5264	264.8729
4	1.7116	-0.0739	-0.2489	0.5215	0.1338	1.478	0.0043	0.0093	0.1239	-0.0023	-0.0372	-0.0353	-0.0434	0.0464	0.0377	0.1463	-0.009	-0.0052	0.0854	-0.0009	0.1189	-60.143	141.668	288.4112
5	0.5985	-0.1176	-0.9488	0.2333	0.328	2.3965	-0.0481	-0.013	-0.0616	0.0871	-0.0094	0.0097	0.1299	0.0788	0.0705	0.1763	-0.0064	-0.0183	0.128	-0.0058	0.189	-55.6582	124.1206	258.6228
6	3.199	-1.4704	0.9571	2.5368	1.0626	2.5055	0.0615	0.2443	0.0018	-0.144	-0.1392	-0.0219	0.0412	-0.1479	0.0655	0.1428	-0.0322	0.017	0.1272	-0.0159	0.1175	-70.2126	134.5921	282.1639
7	1.9719	-0.3151	-0.4827	2.3053	-0.4205	1.6388	-0.0529	-0.2031	0.0136	0.2029	-0.0167	-0.2846	-0.1988	0.45	0.0616	0.1453	-0.0732	-0.0301	0.3141	0.0016	0.1768	-27.7413	143.2101	214.8747
8	0.824	0.0984	-1.4498	0.1938	-0.2486	3.2184	-0.0603	0.0578	-0.071	0.0121	0.0174	-0.0174	0.0338	0.0114	0.0475	0.1421	-0.0197	-0.0252	0.1336	-0.0216	0.1708	-49.1148	132.3286	228.349
9	1.0039	0.0935	-0.304	1.7953	-0.2398	2.0743	0.0138	-0.1242	0.0125	-0.1357	0.1103	0.0937	-0.1432	-0.0267	-0.128	0.1297	-0.0229	-0.0268	0.2461	-0.0204	0.1313	-63.7045	146.6836	195.2801
10	1.1514	0.0812	-1.1721	0.6633	0.4756	3.0264	-0.0359	0.1661	-0.1446	-0.1191	-0.018	-0.0444	-0.0413	0.0123	0.0357	0.2132	-0.034	0.0225	0.166	-0.0467	0.1755	-66.3518	160.3892	232.1512
11	0.0998	-0.1671	-0.7389	0.2745	0.3094	3.7319	0.053	-0.036	0.0654	-0.0378	0.0321	-0.0098	-0.3404	0.1231	-0.0985	0.2347	-0.0873	0.0352	0.2906	-0.069	0.2091	-56.5646	158.0107	203.4058

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 208 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 209 through 359 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 360 through 416 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 8 through 208)
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 209 through 349 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 350 through 416 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 8 through 187 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 188 through 416 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 8 through 208)
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 209 through 318 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 319 through 416 )

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