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- PDB-6bzz: Crystal structure of halogenase PltM in complex with partially bo... -

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Basic information

Entry
Database: PDB / ID: 6bzz
TitleCrystal structure of halogenase PltM in complex with partially bound FAD
Components(Halogenase PltM) x 2
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
FLAVIN-ADENINE DINUCLEOTIDE / Halogenase PltM
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 26, 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 1.4Oct 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 / struct_conn_type
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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)236,79512
Polymers233,4924
Non-polymers3,3038
Water8,197455
1
A: Halogenase PltM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1753
Polymers58,3491
Non-polymers8262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Halogenase PltM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1753
Polymers58,3491
Non-polymers8262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Halogenase PltM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2233
Polymers58,3971
Non-polymers8262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Halogenase PltM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2233
Polymers58,3971
Non-polymers8262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.815, 157.234, 214.008
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Halogenase PltM


Mass: 58349.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4KCZ3, alkylhalidase
#2: Protein Halogenase PltM


Mass: 58397.113 Da / Num. of mol.: 2
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(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4KCZ3, alkylhalidase
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 294 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, soaked in same with 0.5 mM FAD

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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: Jun 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 132527 / % possible obs: 98.2 % / Observed criterion σ(I): 3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.175 / Net I/σ(I): 18.1
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.8 / Num. unique obs: 6252 / CC1/2: 0.786 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BZN

6bzn


Resolution: 2.05→40 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.909 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.186 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24549 6596 5 %RANDOM
Rwork0.21892 ---
obs0.22025 125848 97.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.512 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.05→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15791 0 76 455 16322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01916299
X-RAY DIFFRACTIONr_bond_other_d00.0215380
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.95122123
X-RAY DIFFRACTIONr_angle_other_deg3.704335282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9251997
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4223.577780
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.023152632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.61715116
X-RAY DIFFRACTIONr_chiral_restr0.0690.22409
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02118603
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023983
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_it0.6062.1368009
X-RAY DIFFRACTIONr_mcbond_other0.6052.1357996
X-RAY DIFFRACTIONr_mcangle_it1.1213.29991
X-RAY DIFFRACTIONr_mcangle_other1.1213.29992
X-RAY DIFFRACTIONr_scbond_it0.4812.1978290
X-RAY DIFFRACTIONr_scbond_other0.4812.1978288
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9123.26812132
X-RAY DIFFRACTIONr_long_range_B_refined2.20317.06918308
X-RAY DIFFRACTIONr_long_range_B_other2.14417.04518141
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.051→2.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 428 -
Rwork0.295 8248 -
obs--87.81 %

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