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- PDB-6bzi: Crystal structure of halogenase PltM in complex with ethyl mercur... -

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Basic information

Entry
Database: PDB / ID: 6bzi
TitleCrystal structure of halogenase PltM in complex with ethyl mercury and mercury
ComponentsHalogenase PltM
KeywordsFLAVOPROTEIN / Halogenase / Chlorinase / Brominase / Iodinase
Function / homology
Function and homology information


alkylhalidase / monooxygenase activity / hydrolase activity / nucleotide binding / metal ion binding
Similarity search - Function
Flavin-dependent halogenase / Tryptophan halogenase / : / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ETHYL MERCURY ION / : / Halogenase PltM
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsPang, A.H. / Garneau-Tsodikova, S. / Tsodikov, O.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1149427 United States
CitationJournal: Nat Commun / Year: 2019
Title: Unusual substrate and halide versatility of phenolic halogenase PltM.
Authors: Mori, S. / Pang, A.H. / Thamban Chandrika, N. / Garneau-Tsodikova, S. / Tsodikov, O.V.
History
DepositionDec 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 10, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Halogenase PltM
B: Halogenase PltM
C: Halogenase PltM
D: Halogenase PltM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,68544
Polymers233,3964
Non-polymers7,28940
Water8,125451
1
A: Halogenase PltM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,11511
Polymers58,3491
Non-polymers1,76610
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Halogenase PltM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,54513
Polymers58,3491
Non-polymers2,19612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Halogenase PltM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8819
Polymers58,3491
Non-polymers1,5318
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Halogenase PltM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,14411
Polymers58,3491
Non-polymers1,79510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.722, 156.338, 216.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Halogenase PltM


Mass: 58349.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The N terminal sequence is the cloning tag.
Source: (gene. exp.) Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5) (bacteria)
Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: pltM, PFL_2784 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q4KCZ3, alkylhalidase

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Non-polymers , 5 types, 491 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical...
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EMC / ETHYL MERCURY ION


Mass: 229.651 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H5Hg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris pH 8, 0.2 M NaCl, 0.1 M CaCl2 and 12-17% PEG 8000, crystals soaked in the same solution with 1 mM ethylmercury phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 82751 / % possible obs: 96.3 % / Observed criterion σ(I): 2.4 / Redundancy: 6.7 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 11.2
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.71 / Num. unique obs: 3922 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→45 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.886 / SU B: 9.346 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.56 / ESU R Free: 0.287 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25603 4092 5 %RANDOM
Rwork0.20933 ---
obs0.21165 78214 96.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.704 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.4→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15565 0 71 451 16087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01916073
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215238
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.94521738
X-RAY DIFFRACTIONr_angle_other_deg0.9053.00234916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06951972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32423.546767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3152595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.43115114
X-RAY DIFFRACTIONr_chiral_restr0.0670.22379
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02118296
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023930
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_it0.9852.7127911
X-RAY DIFFRACTIONr_mcbond_other0.9852.7127899
X-RAY DIFFRACTIONr_mcangle_it1.7544.0619868
X-RAY DIFFRACTIONr_mcangle_other1.7534.0629869
X-RAY DIFFRACTIONr_scbond_it1.3162.8488162
X-RAY DIFFRACTIONr_scbond_other1.3162.8488162
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7474.21711871
X-RAY DIFFRACTIONr_long_range_B_refined3.44120.99817522
X-RAY DIFFRACTIONr_long_range_B_other3.44120.99817522
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 263 -
Rwork0.262 5441 -
obs--91.82 %

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