PDB-2og1: Crystal Structure of BphD, a C-C hydrolase from Burkholderia xeno...

ID or keywords:

Entry

Database: PDB / ID: 2og1

Title

Crystal Structure of BphD, a C-C hydrolase from Burkholderia xenovorans LB400

Components

2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase

Keywords

HYDROLASE / BphD /

alpha/beta hydrolase / PCB Degradation / Meta cleavage product hydrolase / MCP hydrolase / 2-hydroxy-6-oxo-6-phenylhexa-2 / 4-dienoate hydrolase

Function / homology

Function and homology information

2-hydroxy-6-oxonona-2,4-dienedioate hydrolase activity /

2,6-dioxo-6-phenylhexa-3-enoate hydrolase /

2,6-dioxo-6-phenylhexa-3-enoate hydrolase activity / aromatic compound catabolic process
Similarity search - Function

Biological species

Burkholderia xenovorans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.6 Å

Authors

Dai, S. / Ke, J. / Bolin, J.T.

Citation

Journal: Biochemistry / Year: 2006
Title: Kinetic and structural insight into the mechanism of BphD, a C-C bond hydrolase from the biphenyl degradation pathway
Authors: Horsman, G.P. / Ke, J. / Dai, S. / Seah, S.Y. / Bolin, J.T. / Eltis, L.D.

History

Deposition	Jan 4, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 16, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.4	Dec 27, 2023	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/og/2og1 ftp://data.pdbj.org/pub/pdb/validation_reports/og/2og1	HTTPS FTP

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Related structure data

Similar structure data	2puh-1 3v1m-1 2rhw-1 2rht-1 3v1l-1 2pu5-1 3v1k-1 2ri6-1 5jz9-1 5jzb-1 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

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PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#165 - Sep 2013 Designed Protein Cages similarity (3) #220 - Apr 2018 Dehalogenases similarity (3) #13 - Jan 2001 Alcohol Dehydrogenase similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #44 - Aug 2003 Calmodulin similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

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Related items in Molecule of the Month

#165 - Sep 2013
Designed Protein Cages
similarity (3)
#220 - Apr 2018
Dehalogenases
similarity (3)
#13 - Jan 2001
Alcohol Dehydrogenase
similarity (1)
#191 - Nov 2015
Glutamate-gated Chloride Receptors
similarity (1)
#233 - May 2019
S-Nitrosylated Hemoglobin
similarity (1)
#44 - Aug 2003
Calmodulin
similarity (1)
#216 - Dec 2017
Biodegradable Plastic
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase

B: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase

hetero molecules

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

1

A: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase

B: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase

hetero molecules

A: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase

B: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase

hetero molecules

defined by author&software
130 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	135.000, 135.000, 66.725
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	172
Space group name H-M	P6₄

Details

The biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation: 0.5-x, 0.866-y, z.

#1: Protein	2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase Mass: 32068.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Gene: bphD / Plasmid: pSS314 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha References: UniProt: P47229, 2,6-dioxo-6-phenylhexa-3-enoate hydrolase
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-EOH / ETHANOL / Ethanol Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.75 Å³/Da / Density % sol: 54.9 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 2.0-2.4 M ammonium sulfate, 6-10% ethanol, 0.1M Tris-HCl, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
3		1

Diffraction source

Source	Site	Beamline	ID	Wavelength	Wavelength (Å)
SYNCHROTRON	APS	14-BM-D	1	0.9795
SYNCHROTRON	APS	14-BM-D	2		0.9537,0.9793,0.9795

Detector

Type	ID	Detector	Date
ADSC QUANTUM 1	1	CCD	Sep 18, 1998
ADSC QUANTUM 1	2	CCD	Dec 5, 1998

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9795	1
2	0.9537	1
3	0.9793	1

Reflection

D res high: 2 Å / D res low: 50 Å

ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	Num. obs	% possible obs
1	14.5	394207	0.049	1.52	86231	92.1
2	14	409145	0.051	1.46	86832	92.5
3	14.5	424739	0.044	1.37	88908	95.4

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared
4.31	50	96.6	1	0.029	0.931
3.42	4.31	97.9	1	0.039	1.425
2.99	3.42	99.5	1	0.051	1.667
2.71	2.99	99.4	1	0.07	1.576
2.52	2.71	99.6	1	0.094	1.625
2.37	2.52	99.6	1	0.119	1.637
2.25	2.37	99.3	1	0.161	1.713
2.15	2.25	93	1	0.201	1.738
2.07	2.15	77	1	0.237	1.841
2	2.07	59.2	1	0.309	1.902
4.31	50	97.6	2	0.03	1.048
3.42	4.31	98.9	2	0.041	1.263
2.99	3.42	99.5	2	0.053	1.478
2.71	2.99	99.6	2	0.075	1.604
2.52	2.71	99.7	2	0.101	1.543
2.37	2.52	99.8	2	0.125	1.638
2.25	2.37	99.4	2	0.175	1.668
2.15	2.25	93.5	2	0.225	1.592
2.07	2.15	77.8	2	0.267	1.681
2	2.07	59.3	2	0.341	1.882
4.31	50	97.4	3	0.025	0.795
3.42	4.31	98.4	3	0.035	1.231
2.99	3.42	99.5	3	0.046	1.46
2.71	2.99	99.5	3	0.063	1.389
2.52	2.71	99.6	3	0.085	1.507
2.37	2.52	99.7	3	0.105	1.495
2.25	2.37	99.5	3	0.136	1.53
2.15	2.25	98.5	3	0.184	1.572
2.07	2.15	88.5	3	0.208	1.656
2	2.07	72.9	3	0.286	1.739

Reflection

Resolution: 1.6→50 Å / Num. obs: 88125 / % possible obs: 96.6 % / R_merge(I) obs: 0.06 / Χ²: 1.148 / Net I/σ(I): 9.9

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.6-1.63	0.36	3352	1.079	1,2	74.1
1.63-1.66	0.371	3602	1.053	1,2	79.7
1.66-1.69	0.298	4003	1.129	1,2	87.9
1.69-1.72	0.293	4295	1.16	1,2	94.7
1.72-1.76	0.274	4481	1.181	1,2	98.9
1.76-1.8	0.25	4543	1.189	1,2	99.9
1.8-1.85	0.222	4521	1.254	1,2	99.9
1.85-1.9	0.212	4553	1.389	1,2	100
1.9-1.95	0.193	4545	1.441	1,2	100
1.95-2.02	0.149	4554	1.376	1,2	100
2.02-2.09	0.142	4542	1.258	1,2	100
2.09-2.17	0.096	4531	1.101	1,2	100
2.17-2.27	0.104	4551	1.029	1,2	100
2.27-2.39	0.074	4567	0.992	1,2	99.9
2.39-2.54	0.068	4570	1.096	1,2	100
2.54-2.74	0.069	4563	1.099	1,2	99.9
2.74-3.01	0.057	4572	1.109	1,2	99.9
3.01-3.45	0.044	4578	0.983	1,2	99.9
3.45-4.34	0.037	4613	1.126	1,2	99.9
4.34-50	0.031	4589	0.894	1,2	97.5

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3

Phasing MAD

D res high: 3.5 Å / D res low: 20 Å / FOM : 0.92 / Reflection: 8863

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	3 wavelength	1	0.9795	4.44	-12.11
1	3 wavelength	2	0.9793	6.83	-11.93
1	3 wavelength	3	0.9537	5.34	-3.82

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	LAM2	28.39	0.659	0.209	0.002	0.574
2	LAM2	30.922	0.52	0.22	0.05	0.663
3	LAM2	60	0.905	0.495	0.29	0.794
4	LAM2	51.183	0.603	0.184	0.152	0.638
5	LAM2	60	0.95	0.269	0.062	0.66
6	LAM2	60	0.589	0.074	0.016	0.82
7	LAM2	60	0.071	0.465	0.151	0.832
8	LAM2	43.638	0.487	0.184	0.247	0.552
9	LAM2	43.278	0.48	0.007	0.004	0.495
10	LAM2	38.33	0.613	0.18	0.258	0.566
11	LAM2	60	0.285	0.357	0.195	0.444
12	LAM2	55.705	0.973	0.475	0.106	0.447
13	LAM2	60	0.375	0.318	0.295	0.469
14	LAM2	60	0.387	0.319	0.194	0.654
15	LAM2	51.413	0.965	0.328	0.095	0.461
16	LAM2	60	0.11	0.39	0.124	0.73
17	LAM2	34.494	0.519	0.165	0.017	0.352
18	LAM2	60	0.076	0.487	0.101	0.651
19	LAM2	60	0.833	0.368	0.309	0.27

Phasing MAD shell

Resolution (Å)	FOM	Reflection
11.16-20	0.9	500
7.54-11.16	0.94	761
6.04-7.54	0.94	952
5.18-6.04	0.95	1089
4.61-5.18	0.92	1221
4.19-4.61	0.92	1333
3.87-4.19	0.91	1470
3.61-3.87	0.92	1537

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	1.17	phasing
CNS	1.1	refinement
PDB_EXTRACT	2	data extraction
ADSC	QUANTUM	data collection

Refinement

Method to determine structure:

MAD / Resolution: 1.6→19.87 Å / R_factor R_free error: 0.002 / Data cutoff high absF: 2428265.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.224	8856	10 %	RANDOM
R_work	0.208	-	-	-
obs	-	88125	96.6 %	-

Solvent computation

Solvent model: FLAT MODEL / B_sol: 50.249 Å² / k_sol: 0.342 e/Å³

Displacement parameters

B_iso mean: 27.1 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.32 Å²	1.25 Å²	0 Å²
2-	-	0.32 Å²	0 Å²
3-	-	-	-0.64 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.22 Å	0.2 Å
Luzzati d res low	-	5 Å
Luzzati sigma a	0.16 Å	0.15 Å

Refinement step

Cycle: LAST / Resolution: 1.6→19.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4492	0	35	469	4996

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target
X-RAY DIFFRACTION	c_bond_d	0.005
X-RAY DIFFRACTION	c_angle_deg	1.2
X-RAY DIFFRACTION	c_dihedral_angle_d	23.1
X-RAY DIFFRACTION	c_improper_angle_d	0.7
X-RAY DIFFRACTION	c_mcbond_it	1.12	1.5
X-RAY DIFFRACTION	c_mcangle_it	1.77	2
X-RAY DIFFRACTION	c_scbond_it	1.76	2
X-RAY DIFFRACTION	c_scangle_it	2.72	2.5

LS refinement shell

Resolution: 1.6→1.7 Å / R_factor R_free error: 0.008 / Total num. of bins used: 6

	R_factor	Num. reflection	% reflection
R_free	0.292	1262	10.2 %
R_work	0.269	11071	-
obs	-	12333	81.5 %

Xplor file

Refine-ID	Serial no	Param file	Topol file
X-RAY DIFFRACTION	1	protein_rep.param	protein.top
X-RAY DIFFRACTION	2	water_rep.param	water.top
X-RAY DIFFRACTION	3	ion.param	ion.top
X-RAY DIFFRACTION	4	ligand.par	ligand.top

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