PDB-6xk1: Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S Apo form

ID or keywords:

Entry

Database: PDB / ID: 6xk1

Title

Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S Apo form

Components

Biuret hydrolase

Keywords

HYDROLASE /

TrtA / BiuH /

triuret /

biuret / cysteine hydrolase /

nitrogen

Function / homology

Isochorismatase-like / Isochorismatase-like superfamily /

Isochorismatase family /

hydrolase activity / Biuret hydrolase

Function and homology information

Biological species

Rhodococcus sp. Mel (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Tassoulas, L.T. / Elias, M.H. / Wackett, L.P.

Funding support

United States, 2items

Organization	Grant number	Country
United States Department of Agriculture (USDA)	2019-67019-29403	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	5T32GM008347-28	United States

Citation

Journal: J.Biol.Chem. / Year: 2020
Title: Discovery of an ultraspecific triuret hydrolase (TrtA) establishes the triuret biodegradation pathway.
Authors: Tassoulas, L.J. / Elias, M.H. / Wackett, L.P.

History

Deposition	Jun 25, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 18, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jul 14, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Oct 18, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6xk1.cif.gz	194 KB	Display	PDBx/mmCIF format
PDB format	pdb6xk1.ent.gz	147.4 KB	Display	PDB format
PDBx/mmJSON format	6xk1.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/xk/6xk1 ftp://data.pdbj.org/pub/pdb/validation_reports/xk/6xk1	HTTPS FTP

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Related structure data

Related structure data	6xixC 6xj4C 6xjeC 6xjmSC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6xjm-d 6azq-2 3ikl-d 6azn-1 3ml1-d 6azs-d 7c67-d 7c64-d 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: Biuret hydrolase

B: Biuret hydrolase

C: Biuret hydrolase

D: Biuret hydrolase

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, dimer of dimers

Unit cell

Length a, b, c (Å)	62.100, 104.400, 135.300
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	Chains AAA BBB
2	1	Chains AAA CCC
3	1	Chains AAA DDD
4	1	Chains BBB CCC
5	1	Chains BBB DDD
6	1	Chains CCC DDD

#1: Protein	Biuret hydrolase / cysteine hydrolase Mass: 26044.336 Da / Num. of mol.: 4 / Mutation: C169S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. Mel (bacteria) / Gene: biuH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H8ZKV9
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.1 Å³/Da / Density % sol: 41.39 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1uL 10mg/mL protein + 1uL 18% w/v PEG3350, 0.2M MgCl2, 1mM triuret pH 5.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.99184 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2020
Radiation	Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99184 Å / Relative weight: 1
Reflection	Resolution: 1.7→82.66 Å / Num. obs: 186186 / % possible obs: 99.6 % / Redundancy: 3.85 % / R_merge(I) obs: 0.077 / Net I/σ(I): 11.55
Reflection shell	Resolution: 1.7→1.8 Å / Redundancy: 3.77 % / R_merge(I) obs: 0.501 / Mean I/σ(I) obs: 2.96 / Num. unique obs: 29499 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS	BUILT=20200131	data reduction
XSCALE	BUILT=20200131	data scaling
MOLREP	11	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6XJM

6xjm

Resolution: 1.7→56.837 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.951 / WR_factor R_free: 0.21 / WR_factor R_work: 0.185 / SU B: 2.108 / SU ML: 0.069 / Average fsc free: 0.9342 / Average fsc work: 0.9422 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.102
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2079	4864	5 %
R_work	0.1844	92409	-
all	0.186	-	-
obs	-	97273	99.858 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 18.828 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.838 Å²	-0 Å²	0 Å²
2-	-	-0.422 Å²	-0 Å²
3-	-	-	-0.416 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→56.837 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6856	0	0	509	7365

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.013	7013
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	6459
X-RAY DIFFRACTION	r_angle_refined_deg	1.647	1.645	9562
X-RAY DIFFRACTION	r_angle_other_deg	1.394	1.575	14926
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.989	5	907
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.121	20.575	348
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.261	15	1073
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.882	15	60
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	950
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	7985
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1483
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	1170
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.188	0.2	5675
X-RAY DIFFRACTION	r_nbtor_refined	0.149	0.2	3397
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	2684
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.113	0.2	296
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.112	0.2	4
X-RAY DIFFRACTION	r_nbd_other	0.178	0.2	24
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.306	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	1.535	1.893	3640
X-RAY DIFFRACTION	r_mcbond_other	1.534	1.892	3639
X-RAY DIFFRACTION	r_mcangle_it	2.106	2.832	4543
X-RAY DIFFRACTION	r_mcangle_other	2.106	2.833	4544
X-RAY DIFFRACTION	r_scbond_it	2.234	2.08	3373
X-RAY DIFFRACTION	r_scbond_other	2.234	2.081	3374
X-RAY DIFFRACTION	r_scangle_it	3.206	3.041	5019
X-RAY DIFFRACTION	r_scangle_other	3.206	3.042	5020
X-RAY DIFFRACTION	r_lrange_it	4.064	22.4	7494
X-RAY DIFFRACTION	r_lrange_other	4.043	22.241	7411
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.065	0.05	6958
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.062	0.05	6978
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.067	0.05	6989
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.066	0.05	6973
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.072	0.05	6966
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.071	0.05	7029

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 (%)
1.7-1.744	0.295	357	0.279	6788	X-RAY DIFFRACTION	99.958
1.744-1.792	0.255	346	0.23	6575	X-RAY DIFFRACTION	100
1.792-1.844	0.24	339	0.215	6436	X-RAY DIFFRACTION	100
1.844-1.901	0.238	328	0.203	6226	X-RAY DIFFRACTION	99.9542
1.901-1.963	0.26	317	0.229	6036	X-RAY DIFFRACTION	99.9371
1.963-2.032	0.236	308	0.189	5844	X-RAY DIFFRACTION	99.9188
2.032-2.108	0.225	297	0.196	5646	X-RAY DIFFRACTION	99.8824
2.108-2.194	0.236	287	0.197	5444	X-RAY DIFFRACTION	99.8084
2.194-2.292	0.241	275	0.199	5236	X-RAY DIFFRACTION	99.7466
2.292-2.404	0.204	262	0.175	4978	X-RAY DIFFRACTION	99.7146
2.404-2.534	0.213	251	0.172	4766	X-RAY DIFFRACTION	99.7217
2.534-2.687	0.224	238	0.182	4517	X-RAY DIFFRACTION	99.7483
2.687-2.872	0.201	224	0.176	4259	X-RAY DIFFRACTION	99.8219
2.872-3.102	0.2	210	0.187	3983	X-RAY DIFFRACTION	99.8096
3.102-3.398	0.196	192	0.185	3654	X-RAY DIFFRACTION	99.8183
3.398-3.798	0.184	176	0.172	3342	X-RAY DIFFRACTION	99.8581
3.798-4.384	0.142	156	0.143	2973	X-RAY DIFFRACTION	99.6814
4.384-5.366	0.146	133	0.147	2529	X-RAY DIFFRACTION	99.85
5.366-7.572	0.215	106	0.181	2003	X-RAY DIFFRACTION	100

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