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- PDB-6bzt: Crystal structure of halogenase PltM L111Y mutant in complex with FAD -

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Basic information

Entry
Database: PDB / ID: 6bzt
TitleCrystal structure of halogenase PltM L111Y mutant in complex with FAD
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
BROMIDE ION / FLAVIN-ADENINE DINUCLEOTIDE / Halogenase PltM
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
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.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)237,71524
Polymers233,5974
Non-polymers4,11920
Water16,988943
1
A: Halogenase PltM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5808
Polymers58,3991
Non-polymers1,1817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Halogenase PltM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4206
Polymers58,3991
Non-polymers1,0215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Halogenase PltM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3805
Polymers58,3991
Non-polymers9814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Halogenase PltM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3355
Polymers58,3991
Non-polymers9364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.974, 157.462, 213.036
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: 58399.129 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The N-terminal sequence is a 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

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Non-polymers , 5 types, 963 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 943 / 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: 46.45 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris pH 8, 0.2 M NaBr, 0.1 M CaCl2 and 14% PEG 8000, cryoprotection in same except for additional 20% PEG 400 and 1 mM FAD overnight

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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: 2.1→50 Å / Num. obs: 119974 / % possible obs: 94.7 % / Observed criterion σ(I): 1.9 / Redundancy: 5.4 % / Rmerge(I) obs: 0.197 / Net I/σ(I): 10.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.3 % / Num. unique obs: 5827 / CC1/2: 0.568 / % possible all: 92.6

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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: 2.1→35 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.118 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.206 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 5971 5 %RANDOM
Rwork0.20726 ---
obs0.2091 113768 94.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.901 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.1→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15844 0 228 943 17015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01916548
X-RAY DIFFRACTIONr_bond_other_d0.0060.0215530
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.9622512
X-RAY DIFFRACTIONr_angle_other_deg0.917335644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95552014
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13123.62790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.408152648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.54815116
X-RAY DIFFRACTIONr_chiral_restr0.0680.22447
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02118846
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024050
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_it0.6622.4418051
X-RAY DIFFRACTIONr_mcbond_other0.6622.448046
X-RAY DIFFRACTIONr_mcangle_it1.2253.65510064
X-RAY DIFFRACTIONr_mcangle_other1.2253.65610065
X-RAY DIFFRACTIONr_scbond_it0.5332.5368497
X-RAY DIFFRACTIONr_scbond_other0.5332.5368498
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9783.77612449
X-RAY DIFFRACTIONr_long_range_B_refined3.10419.93619213
X-RAY DIFFRACTIONr_long_range_B_other2.95319.83318900
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 460 -
Rwork0.271 8075 -
obs--92.7 %

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