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- PDB-6apg: Trans-acting transferase from Disorazole synthase with malonate -

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Basic information

Entry
Database: PDB / ID: 6apg
TitleTrans-acting transferase from Disorazole synthase with malonate
ComponentsDisD protein
KeywordsTRANSFERASE / acyl transferase / Disorazole synthase / polyketide synthase / malonate complex
Function / homology
Function and homology information


[acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity
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
MALONATE ION / [acyl-carrier-protein] S-malonyltransferase
Similarity search - Component
Biological speciesSorangium cellulosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMathews, I.I. / Lyubimov, A.Y. / Soltis, S.M. / Khosla, C. / Robbins, T. / Cohen, A.E.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM087934 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 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6909
Polymers61,0702
Non-polymers6207
Water6,161342
1
A: DisD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8655
Polymers30,5351
Non-polymers3304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DisD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8254
Polymers30,5351
Non-polymers2903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.670, 104.670, 138.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DisD protein / DszD


Mass: 30534.912 Da / Num. of mol.: 2 / Fragment: transferase domain (UNP residues 1-281)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorangium cellulosum (bacteria) / Gene: dszD, disD / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4U443

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Non-polymers , 5 types, 349 molecules

#2: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 3.11 Å3/Da / Density % sol: 60.43 %
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9761 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 14, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9761 Å / Relative weight: 1
ReflectionResolution: 2→39.2 Å / Num. obs: 52610 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.054 % / Biso Wilson estimate: 31.576 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.117 / Χ2: 0.986 / Net I/σ(I): 15.42
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.058.1890.8412.838310.8340.89699.8
2.05-2.118.1880.6693.4737330.8710.71399.9
2.11-2.178.1720.5534.1536230.9040.59100
2.17-2.248.1670.4624.9735320.9370.49399.9
2.24-2.318.1810.3985.8834180.950.42599.9
2.31-2.398.1490.3196.9733430.9660.34100
2.39-2.488.1980.282831950.9750.30199.9
2.48-2.588.1690.2528.8430750.9810.26999.9
2.58-2.78.1390.20210.8729910.9860.216100
2.7-2.838.1260.16213.1628480.9920.173100
2.83-2.988.1250.12516.4427200.9950.134100
2.98-3.168.0630.09720.1325780.9970.103100
3.16-3.388.0380.07325.4624290.9980.078100
3.38-3.657.9840.05731.4122540.9990.061100
3.65-47.9090.04636.8421140.9990.049100
4-4.477.7420.03941.3619130.9990.042100
4.47-5.167.4280.03940.3816930.9990.042100
5.16-6.327.7070.04536.2414760.9990.049100
6.32-8.947.570.03542.4111570.9990.038100
8.94-39.26.7830.02546.1568710.02798.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code: 3RGI

3rgi


Resolution: 2→39.2 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.7 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.124
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 2631 5 %RANDOM
Rwork0.1839 ---
obs0.1847 49979 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.7 Å2 / Biso mean: 27.849 Å2 / Biso min: 15.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å2-0 Å2-0 Å2
2--0.85 Å2-0 Å2
3----1.71 Å2
Refinement stepCycle: final / Resolution: 2→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4284 0 37 345 4666
Biso mean--42.39 33.89 -
Num. residues----562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194398
X-RAY DIFFRACTIONr_bond_other_d0.0010.024140
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.9765935
X-RAY DIFFRACTIONr_angle_other_deg0.92539545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1625560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.01622.864199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27915715
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4341543
X-RAY DIFFRACTIONr_chiral_restr0.070.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214995
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02952
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 191 -
Rwork0.243 3627 -
all-3818 -
obs--99.71 %
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)
10.4140.05220.02430.912-0.43060.8877-0.0393-0.0291-0.0197-0-0.0065-0.0208-0.02530.09830.04580.0083-0.0006-0.0090.040.00390.0278124.859251.842-122.3701
20.30490.0310.13750.98880.49170.988-0.04040.0406-0.0056-0.001-0.02450.064-0.0182-0.11860.06490.0094-0.0139-0.00870.05280.00180.045284.891148.7405-120.3941
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 281
2X-RAY DIFFRACTION2B1 - 281

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