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- PDB-5zk4: The structure of DSZS acyltransferase with carrier protein -

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Basic information

Entry
Database: PDB / ID: 5zk4
TitleThe structure of DSZS acyltransferase with carrier protein
Components
  • DisA protein
  • DisD protein
KeywordsTRANSFERASE / ACYL CARRIER PROTEIN / POLYKETIDE BIOSYNTHESIS
Function / homology
Function and homology information


[acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / metal ion binding / cytosol
Similarity search - Function
: / [Acyl-carrier-protein] S-malonyltransferase, inserted helical domain / PfaD family protein / Malonyl CoA-acyl carrier protein transacylase, FabD-type / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Methyltransferase type 12 / Methyltransferase domain / PKS_PP_betabranch ...: / [Acyl-carrier-protein] S-malonyltransferase, inserted helical domain / PfaD family protein / Malonyl CoA-acyl carrier protein transacylase, FabD-type / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Methyltransferase type 12 / Methyltransferase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Aldolase-type TIM barrel / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9EF / [acyl-carrier-protein] S-malonyltransferase / DisA protein
Similarity search - Component
Biological speciesSorangium cellulosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsMiyanaga, A. / Ouchi, R. / Kudo, F. / Eguchi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17K07747 Japan
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Structural basis of protein-protein interactions between a trans-acting acyltransferase and acyl carrier protein in polyketide disorazole biosynthesis
Authors: Miyanaga, A. / Ouchi, R. / Ishikawa, F. / Goto, E. / Tanabe, G. / Kudo, F. / Eguchi, T.
History
DepositionMar 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.2Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_CSD / _citation.journal_id_ISSN ..._citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DisD protein
B: DisD protein
C: DisA protein
D: DisA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,67016
Polymers86,9434
Non-polymers1,72712
Water4,882271
1
A: DisD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8916
Polymers33,1231
Non-polymers7685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13070 Å2
MethodPISA
2
B: DisD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8916
Polymers33,1231
Non-polymers7685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-17 kcal/mol
Surface area12820 Å2
MethodPISA
3
C: DisA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4452
Polymers10,3491
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5140 Å2
MethodPISA
4
D: DisA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4452
Polymers10,3491
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.324, 96.629, 99.056
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 DisD protein / DszD


Mass: 33122.930 Da / Num. of mol.: 2 / Mutation: S86C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorangium cellulosum (bacteria) / Gene: dszD, disD / Plasmid: PCold I / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4U443
#2: Protein DisA protein / DszA


Mass: 10348.558 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorangium cellulosum (bacteria) / Gene: dszA, disA / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4U447
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-9EF / N-[2-(acetylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide


Mass: 383.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H26N3O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2M ammonium sulfate and 5% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2018
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 56711 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.9
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 2 / Num. unique obs: 4114 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SBM

3sbm


Resolution: 2.03→48.36 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.873 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.152 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22236 2801 4.9 %RANDOM
Rwork0.18291 ---
obs0.18483 53843 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.473 Å2
Baniso -1Baniso -2Baniso -3
1--2.25 Å20 Å20 Å2
2--1.1 Å2-0 Å2
3---1.15 Å2
Refinement stepCycle: 1 / Resolution: 2.03→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 98 271 5939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0195758
X-RAY DIFFRACTIONr_bond_other_d0.0090.025542
X-RAY DIFFRACTIONr_angle_refined_deg1.991.9887780
X-RAY DIFFRACTIONr_angle_other_deg1.0283.00312680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9225714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.32122.593270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.82415946
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8751566
X-RAY DIFFRACTIONr_chiral_restr0.1370.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216522
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021348
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 222 -
Rwork0.244 3889 -
obs--100 %
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)
10.47740.12870.25270.61120.04340.4639-0.0273-0.04150.02010.0338-0.00660.00640.0172-0.07760.03390.17980.00380.00710.0139-0.00610.003445.34359.146.994
20.71260.1611-0.05210.3464-0.25220.2277-0.04150.0620.0396-0.0514-0.0082-0.04620.0771-0.00290.04970.2109-0.0050.00650.01430.00250.015332.84375.111-31.771
32.3177-1.61181.23313.0351-1.41191.4325-0.2041-0.43430.22290.270.196-0.074-0.1471-0.37370.00820.22330.0601-0.03530.1698-0.04890.058629.46482.194-0.188
44.7201-2.11380.35783.671-1.63180.88820.18440.3876-0.0399-0.5808-0.2571-0.23870.30330.06410.07270.33920.04720.08640.03710.01760.094755.03558.214-24.453
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 304
2X-RAY DIFFRACTION2B-1 - 304
3X-RAY DIFFRACTION3C7 - 102
4X-RAY DIFFRACTION4D7 - 102

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