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- PDB-6apf: Trans-acting transferase from Disorazole synthase complexed with ... -

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Basic information

Entry
Database: PDB / ID: 6apf
TitleTrans-acting transferase from Disorazole synthase complexed with Citrate.
ComponentsDisD protein
KeywordsTRANSFERASE / acyl transferase / Disorazole synthase / citrate complex / polyketide synthase
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
PfaD family protein / : / [Acyl-carrier-protein] S-malonyltransferase, inserted helical domain / 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 ...PfaD family protein / : / [Acyl-carrier-protein] S-malonyltransferase, inserted helical domain / 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 / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / 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
CITRIC ACID / [acyl-carrier-protein] S-malonyltransferase
Similarity search - Component
Biological speciesSorangium cellulosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsMathews, I.I. / Lyubimov, A. / Soltis, M. / Khosla, C. / Cohen, A. / Robbins, T.
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 / 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
B: DisD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,19912
Polymers61,0702
Non-polymers1,12910
Water10,070559
1
A: DisD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0996
Polymers30,5351
Non-polymers5645
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DisD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0996
Polymers30,5351
Non-polymers5645
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.260, 104.260, 138.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#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
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 3.09 Å3/Da / Density % sol: 60.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.6M Ammonium Sulfate, 100 mM sodium citrate (pH 4.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.63→39.17 Å / Num. obs: 95319 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.46 % / Biso Wilson estimate: 27.963 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.073 / Χ2: 1.025 / Net I/σ(I): 18.91 / Num. measured all: 615784 / Scaling rejects: 59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.63-1.675.990.9822.0769650.6981.07899.9
1.67-1.725.7650.8322.5467890.7750.91699.8
1.72-1.776.6010.6283.5165890.8560.68399.9
1.77-1.826.6990.4924.6264370.90.534100
1.82-1.886.6520.4085.5362380.9310.443100
1.88-1.956.5350.3217.1160350.9550.35100
1.95-2.026.1360.2439.1458210.970.26699.7
2.02-2.16.6720.17312.656160.9850.18899.9
2.1-2.26.890.13715.6754070.9890.149100
2.2-2.316.8110.11218.4351720.9930.122100
2.31-2.436.6880.08922.4349280.9960.09799.9
2.43-2.586.2450.07923.8446520.9960.08699.7
2.58-2.766.5470.06429.0144000.9970.06999.7
2.76-2.986.8510.0535.3741030.9980.05499.8
2.98-3.266.6020.0441.8538000.9990.04399.6
3.26-3.646.2290.03248.5334290.9990.03599.4
3.64-4.216.1480.02655.6530350.9990.02898.7
4.21-5.156.6480.0236126200.9990.02599.6
5.15-7.296.0770.02354.4820800.9990.02599.4
7.29-39.176.3260.01962.6120310.02197.9

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Processing

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

3rgi


Resolution: 1.63→39.17 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.019 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.074
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1914 4766 5 %RANDOM
Rwork0.1675 ---
obs0.1687 90553 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.24 Å2 / Biso mean: 21.835 Å2 / Biso min: 12.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å2-0 Å2-0 Å2
2--0.24 Å2-0 Å2
3----0.48 Å2
Refinement stepCycle: final / Resolution: 1.63→39.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4284 0 72 563 4919
Biso mean--38.61 33.69 -
Num. residues----562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194470
X-RAY DIFFRACTIONr_bond_other_d0.0020.024190
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9836037
X-RAY DIFFRACTIONr_angle_other_deg0.94239671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0295570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.71522.935201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35815721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8111543
X-RAY DIFFRACTIONr_chiral_restr0.1920.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215081
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02962
LS refinement shellResolution: 1.63→1.672 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 347 -
Rwork0.267 6608 -
all-6955 -
obs--99.87 %
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)
10.08430.05780.01690.3173-0.19960.3573-0.0304-0.0194-0.0099-0.0115-0.0012-0.0039-0.02450.05330.03150.01390.0016-0.00140.03060.01510.0166124.36751.623-122.567
20.08220.00040.12120.40540.22140.3714-0.03030.00430.0050.0083-0.00150.0225-0.0222-0.04960.03180.0164-0.0152-0.00230.0427-0.00810.016584.54148.659-120.395
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 281
2X-RAY DIFFRACTION2B1 - 281

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