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- PDB-6apk: Trans-acting transferase from Disorazole synthase solved by seria... -

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Basic information

Entry
Database: PDB / ID: 6apk
TitleTrans-acting transferase from Disorazole synthase solved by serial femtosecond XFEL crystallography
ComponentsDisD protein
KeywordsTRANSFERASE / Disorazole synthase / XFEL crystal structure / serial femtosecond crystallography
Function / homology
Function and homology information


[acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase 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 / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase ...: / [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 / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Aldolase-type TIM barrel / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
[acyl-carrier-protein] S-malonyltransferase
Similarity search - Component
Biological speciesSorangium cellulosum (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsLyubimov, A.Y. / Mathews, I.I. / Uervivojnangkoorn, M. / Khosla, C. / Soltis, S.M. / Cohen, A.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
CitationJournal: Biochemistry / Year: 2017
Title: The Conformational Flexibility of the Acyltransferase from the Disorazole Polyketide Synthase Is Revealed by an X-ray Free-Electron Laser Using a Room-Temperature Sample Delivery Method for Serial Crystallography.
Authors: Mathews, I.I. / Allison, K. / Robbins, T. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Brunger, A.T. / Khosla, C. / DeMirci, H. / McPhillips, S.E. / Hollenbeck, M. / Soltis, M. / Cohen, A.E.
History
DepositionAug 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 2.0Apr 11, 2018Group: Data collection / Polymer sequence / Category: diffrn_source / entity_poly
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_target_identifier
Revision 2.1Nov 28, 2018Group: Data collection
Category: diffrn / pdbx_serial_crystallography_sample_delivery / pdbx_serial_crystallography_sample_delivery_fixed_target
Item: _diffrn.pdbx_serial_crystal_experiment
Revision 2.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DisD protein


Theoretical massNumber of molelcules
Total (without water)30,6631
Polymers30,6631
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.214, 54.642, 124.152
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: 30663.041 Da / Num. of mol.: 1 / Fragment: UNP residues 1-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorangium cellulosum (bacteria) / Strain: SO CE12 / Gene: dszD, disD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q4U443, [acyl-carrier-protein] S-malonyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.6M Ammonium Sulphate, 100mM sodium citrate (pH 4.5)

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: XPP / Wavelength: 1.3013 Å
DetectorType: RAYONIX MX170-HS / Detector: CCD / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3013 Å / Relative weight: 1
ReflectionResolution: 2.5→19.5 Å / Num. obs: 10781 / % possible obs: 98.8 % / Redundancy: 14.2 % / Biso Wilson estimate: 3.09 Å2 / CC1/2: 0.92 / Net I/σ(I): 4.1
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.79 / % possible all: 89.9
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetMotion control: DCSS / Sample holding: Crystal/Sample Extractor

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.32 Å19.49 Å
Translation4.32 Å19.49 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
PHASER2.7.16phasing
PDB_EXTRACT3.22data extraction
cctbx.xfeldata reduction
cctbx.primedata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RGI

3rgi


Resolution: 2.5→19.499 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 20.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2694 1080 10.02 %
Rwork0.2254 --
obs0.2298 10781 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→19.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 0 0 73 2221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032209
X-RAY DIFFRACTIONf_angle_d0.6362989
X-RAY DIFFRACTIONf_dihedral_angle_d20.5431338
X-RAY DIFFRACTIONf_chiral_restr0.118324
X-RAY DIFFRACTIONf_plane_restr0.004401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.61360.34351270.29011130X-RAY DIFFRACTION94
2.6136-2.7510.33721300.27411182X-RAY DIFFRACTION98
2.751-2.92290.29631340.27161198X-RAY DIFFRACTION100
2.9229-3.14770.2941340.23781200X-RAY DIFFRACTION100
3.1477-3.46280.2931350.21761215X-RAY DIFFRACTION99
3.4628-3.96030.23381360.19551227X-RAY DIFFRACTION100
3.9603-4.97580.20221380.16881244X-RAY DIFFRACTION100
4.9758-19.49960.21051460.19431305X-RAY DIFFRACTION99
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)
10.05710.05760.00370.07580.01990.01880.05180.0478-0.0898-0.01860.080.07990.01180.02690.03890.2350.03710.03490.08550.04070.160738.928621.268717.1364
20.0001-0.0043-0.00810.00230.00890.0149-0.0193-0.01530.0695-0.0881-0.01460.06750.08460.0046-0.08360.091-0.06610.18220.0863-0.0169-0.07940.794219.73154.7314
30.0401-0.01510.00540.01220.01070.0240.00280.08140.11940.005-0.07350.0201-0.0052-0.0087-0.0565-0.1141-0.1002-0.06280.0183-0.0350.017729.796820.534111.1217
40.01150.0157-0.00070.04340.00520.0391-0.03250.01880.0408-0.0785-0.07610.0764-0.00160.0566-0.1181-0.0214-0.1407-0.0734-0.0725-0.01540.06435.854444.236323.1999
50.00020.00130.0041-0.0002-0.00230.0148-0.01060.0280.02730.02330.0051-0.0124-0.05-0.0259-0.01690.2672-0.0376-0.14460.2607-0.01710.220221.425635.8196.791
60.0144-0.00780.00610.005-0.00350.0023-0.00230.0065-0.04930.06130.00680.07920.0291-0.0305-0.0028-0.0511-0.14180.02150.1364-0.04570.115819.983620.994217.3534
70.0853-0.0031-0.02420.0398-0.01140.026-0.031-0.0611-0.027-0.0247-0.0243-0.0234-0.00490.0176-0.08270.0833-0.0001-0.02140.0796-0.06040.118631.49824.92125.8067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 73 )
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 117 )
4X-RAY DIFFRACTION4chain 'A' and (resid 118 through 192 )
5X-RAY DIFFRACTION5chain 'A' and (resid 193 through 208 )
6X-RAY DIFFRACTION6chain 'A' and (resid 209 through 231 )
7X-RAY DIFFRACTION7chain 'A' and (resid 232 through 282 )

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