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- PDB-6brm: The crystal structure of isothiocyanate hydrolase from Delia radi... -

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Basic information

Entry
Database: PDB / ID: 6brm
TitleThe crystal structure of isothiocyanate hydrolase from Delia radicum gut bacteria
ComponentsPutative metal-dependent isothiocyanate hydrolase SaxA
KeywordsHYDROLASE / isothiocyanate hydrolase / ITC / SaxA / Drgb3_SaxA
Function / homology
Function and homology information


Beta-lactamase superfamily domain / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Putative metal-dependent isothiocyanate hydrolase SaxA
Similarity search - Component
Biological speciesPectobacterium carotovorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsTan, K. / van den Bosch, T. / Joachimiak, A. / Welte, C.
Funding support United States, Netherlands, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585, GM115586 United States
Nederlandse Organisatie voor Wetenschappelijk OnderzoekSIAM Gravitation Grant 024.002.002 Netherlands
CitationJournal: Appl. Environ. Microbiol. / Year: 2018
Title: Functional Profiling and Crystal Structures of Isothiocyanate Hydrolases Found in Gut-Associated and Plant-Pathogenic Bacteria.
Authors: van den Bosch, T.J.M. / Tan, K. / Joachimiak, A. / Welte, C.U.
History
DepositionNov 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative metal-dependent isothiocyanate hydrolase SaxA
B: Putative metal-dependent isothiocyanate hydrolase SaxA
C: Putative metal-dependent isothiocyanate hydrolase SaxA
D: Putative metal-dependent isothiocyanate hydrolase SaxA
E: Putative metal-dependent isothiocyanate hydrolase SaxA
F: Putative metal-dependent isothiocyanate hydrolase SaxA
G: Putative metal-dependent isothiocyanate hydrolase SaxA
H: Putative metal-dependent isothiocyanate hydrolase SaxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,85928
Polymers241,6288
Non-polymers1,23120
Water75742
1
A: Putative metal-dependent isothiocyanate hydrolase SaxA
B: Putative metal-dependent isothiocyanate hydrolase SaxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7157
Polymers60,4072
Non-polymers3085
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Putative metal-dependent isothiocyanate hydrolase SaxA
D: Putative metal-dependent isothiocyanate hydrolase SaxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7157
Polymers60,4072
Non-polymers3085
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Putative metal-dependent isothiocyanate hydrolase SaxA
F: Putative metal-dependent isothiocyanate hydrolase SaxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7157
Polymers60,4072
Non-polymers3085
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Putative metal-dependent isothiocyanate hydrolase SaxA
H: Putative metal-dependent isothiocyanate hydrolase SaxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7157
Polymers60,4072
Non-polymers3085
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.163, 79.526, 90.408
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative metal-dependent isothiocyanate hydrolase SaxA


Mass: 30203.500 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium carotovorum (bacteria) / Plasmid: pASK-IBA3plus / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0N7FW12
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M calcium acetate, 0.1M HEPES:NaOH, 10% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2017 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.657
11-h,-k,l20.343
ReflectionResolution: 2.55→50 Å / Num. obs: 81359 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 43.54 Å2 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.072 / Rrim(I) all: 0.134 / Χ2: 0.882 / Net I/σ(I): 10.8
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 1.28 / Num. unique obs: 3647 / CC1/2: 0.786 / Rpim(I) all: 0.471 / Rrim(I) all: 0.867 / Χ2: 0.619 / % possible all: 88.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RPC

3rpc


Resolution: 2.55→49.84 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 10.033 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.062 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24335 4076 5 %RANDOM
Rwork0.20558 ---
obs0.20749 77269 97.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.479 Å2
Baniso -1Baniso -2Baniso -3
1--19.11 Å2-0 Å28.03 Å2
2--76.9 Å20 Å2
3----57.79 Å2
Refinement stepCycle: 1 / Resolution: 2.55→49.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16322 0 28 42 16392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01916688
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215615
X-RAY DIFFRACTIONr_angle_refined_deg1.8651.98122824
X-RAY DIFFRACTIONr_angle_other_deg0.875336223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99452078
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08124.878740
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77152856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8791568
X-RAY DIFFRACTIONr_chiral_restr0.0640.22614
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02118429
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023194
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.395.888342
X-RAY DIFFRACTIONr_mcbond_other1.395.888343
X-RAY DIFFRACTIONr_mcangle_it2.3578.81510418
X-RAY DIFFRACTIONr_mcangle_other2.3568.81610411
X-RAY DIFFRACTIONr_scbond_it1.0855.8778346
X-RAY DIFFRACTIONr_scbond_other1.0845.8768339
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9148.75412495
X-RAY DIFFRACTIONr_long_range_B_refined3.62767.89417602
X-RAY DIFFRACTIONr_long_range_B_other3.62767.89717603
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 239 -
Rwork0.345 4945 -
obs--84.87 %

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