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- PDB-5m3k: A multi-component acyltransferase PhlABC from Pseudomonas protegens -

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Basic information

Entry
Database: PDB / ID: 5m3k
TitleA multi-component acyltransferase PhlABC from Pseudomonas protegens
Components
  • 2,4-diacetylphloroglucinol biosynthesis protein PhlB
  • 2,4-diacetylphloroglucinol biosynthesis protein PhlC
  • PhlA
KeywordsTRANSFERASE / acyltransferase / Pseudomonas protegens / PhlABC / multi-component
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Domain of unknown function DUF35, OB-fold, C-terminal / DUF35 OB-fold domain, acyl-CoA-associated / Domain of unknown function DUF35, rubredoxin-like zinc ribbon domain, N-terminal / Rubredoxin-like zinc ribbon domain (DUF35_N) / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase / Thiolase, N-terminal ...Domain of unknown function DUF35, OB-fold, C-terminal / DUF35 OB-fold domain, acyl-CoA-associated / Domain of unknown function DUF35, rubredoxin-like zinc ribbon domain, N-terminal / Rubredoxin-like zinc ribbon domain (DUF35_N) / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase-like / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
2,4-diacetylphloroglucinol biosynthesis protein PhlB / 2,4-diacetylphloroglucinol biosynthesis protein PhlC / Hydroxymethylglutaryl-CoA synthase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsPavkov-Keller, T. / Schmidt, N.G. / Kroutil, W. / Gruber, K.
CitationJournal: Chembiochem / Year: 2019
Title: Structure and Catalytic Mechanism of a Bacterial Friedel-Crafts Acylase.
Authors: Pavkov-Keller, T. / Schmidt, N.G. / Zadlo-Dobrowolska, A. / Kroutil, W. / Gruber, K.
History
DepositionOct 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 27, 2019Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jan 17, 2024Group: 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 / refine_hist / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _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_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PhlA
B: 2,4-diacetylphloroglucinol biosynthesis protein PhlB
C: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
D: PhlA
E: 2,4-diacetylphloroglucinol biosynthesis protein PhlB
F: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,7598
Polymers195,6286
Non-polymers1312
Water7,188399
1
A: PhlA
B: 2,4-diacetylphloroglucinol biosynthesis protein PhlB
C: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
D: PhlA
E: 2,4-diacetylphloroglucinol biosynthesis protein PhlB
F: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
hetero molecules

A: PhlA
B: 2,4-diacetylphloroglucinol biosynthesis protein PhlB
C: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
D: PhlA
E: 2,4-diacetylphloroglucinol biosynthesis protein PhlB
F: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,51716
Polymers391,25512
Non-polymers2624
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area69650 Å2
ΔGint-304 kcal/mol
Surface area94040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.626, 222.626, 237.099
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLEULEUAA4 - 3624 - 362
21LYSLYSLEULEUDD4 - 3624 - 362
12METMETASPASPBB3 - 1453 - 145
22METMETASPASPEE3 - 1453 - 145
13ALAALAASPASPCC3 - 3983 - 398
23ALAALAASPASPFF3 - 3983 - 398

NCS ensembles :
ID
1
2
3

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Components

#1: Protein PhlA


Mass: 38565.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: phlA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9TP23
#2: Protein 2,4-diacetylphloroglucinol biosynthesis protein PhlB


Mass: 16666.434 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: phlB, PFL_5956 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4K419
#3: Protein 2,4-diacetylphloroglucinol biosynthesis protein PhlC


Mass: 42581.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CYS:SCY issue - at the position 88 the Cystein residue is modified and has attached acetyl group (SCY)
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: phlC, PFL_5955 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4K420
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 4.35 Å3/Da / Density % sol: 71.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 12 mg mL-1 protein solution Index screen crystallization condition #91 (0.15 M, DL-malic acid pH 7.0, 20% w/v polyethylene glycol 3,350)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.83→49.862 Å / Num. obs: 82036 / % possible obs: 100 % / Redundancy: 8.5 % / CC1/2: 0.98 / Rmerge(I) obs: 0.255 / Rrim(I) all: 0.271 / Net I/σ(I): 7.87
Reflection shellResolution: 2.83→2.94 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.891 / Mean I/σ(I) obs: 2.23 / CC1/2: 0.67 / Rrim(I) all: 0.271 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0173refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tvz, 3zbg

1tvz

3zbg


Resolution: 2.83→49.862 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 20.171 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.386 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19618 4102 5 %RANDOM
Rwork0.16748 ---
obs0.1689 77934 99.71 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.211 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20.21 Å20 Å2
2--0.43 Å2-0 Å2
3----1.38 Å2
Refinement stepCycle: 1 / Resolution: 2.83→49.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13606 0 2 399 14007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01913874
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212780
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.9618774
X-RAY DIFFRACTIONr_angle_other_deg0.9533.00129614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75851793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64124.08598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.111152267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.821582
X-RAY DIFFRACTIONr_chiral_restr0.0730.22079
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215719
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022795
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_it1.092.4887190
X-RAY DIFFRACTIONr_mcbond_other1.092.4887189
X-RAY DIFFRACTIONr_mcangle_it1.8473.7288977
X-RAY DIFFRACTIONr_mcangle_other1.8473.7298978
X-RAY DIFFRACTIONr_scbond_it1.5392.686684
X-RAY DIFFRACTIONr_scbond_other1.5342.6796682
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5863.9469797
X-RAY DIFFRACTIONr_long_range_B_refined4.50447.89256988
X-RAY DIFFRACTIONr_long_range_B_other4.49447.87956852
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A223400.05
12D223400.05
21B81660.06
22E81660.06
31C252520.06
32F252520.06
LS refinement shellResolution: 2.834→2.907 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 290 -
Rwork0.286 5507 -
obs--97.12 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8475-0.0431-0.05870.3076-0.02520.89320.0166-0.09290.11320.0704-0.01970.0485-0.11-0.06610.00310.10980.00160.01290.0621-0.02020.025259.338-70.78743.187
21.2058-0.07530.49190.4812-0.08010.9814-0.02380.12830.1077-0.04940.01190.046-0.06710.00450.01180.09670.00510.01190.10930.01740.019944.086-90.3520.933
30.3673-0.0529-0.08320.4024-0.13830.8417-0.01280.00280.07840.00160.01610.061-0.082-0.1013-0.00330.1028-0.00540.00750.1002-0.01090.037823.001-95.36522.237
40.47050.0359-0.19760.57360.0280.861-0.01060.11650.062-0.08320.03540.0469-0.0725-0.0464-0.02480.07470.0108-0.01140.08830.01960.011867.615-77.089-9.313
50.60960.42220.03191.22080.41660.80540.0381-0.03180.07950.0139-0.06330.0779-0.0589-0.07140.02520.11470.00770.01190.0798-0.00450.011884.328-60.36833.333
60.4232-0.1298-0.13220.57740.0550.74050.02340.02030.0932-0.0537-0.01870.0188-0.1414-0.0104-0.00480.1166-0.0148-0.00490.09780.01410.0267103.432-51.3311.37
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 362
2X-RAY DIFFRACTION2B3 - 146
3X-RAY DIFFRACTION2B200
4X-RAY DIFFRACTION3C3 - 398
5X-RAY DIFFRACTION4D4 - 362
6X-RAY DIFFRACTION5E2 - 146
7X-RAY DIFFRACTION5E200
8X-RAY DIFFRACTION6F3 - 398

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