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- PDB-6pfn: Succinyl-CoA synthase from Francisella tularensis -

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Basic information

Entry
Database: PDB / ID: 6pfn
TitleSuccinyl-CoA synthase from Francisella tularensis
Components(Succinate--CoA ligase [ADP-forming] subunit ...) x 2
KeywordsLIGASE / Succinyl-CoA synthase / structural genomics / CPX_02187_02692 / IDP02187 / IDP02692 / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / tricarboxylic acid cycle / nucleotide binding / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Succinyl-CoA ligase, alpha subunit / Succinate--CoA synthetase, beta subunit / ATP-grasp fold, succinyl-CoA synthetase-type / ATP-grasp domain / Succinyl-CoA synthetase domains / ATP-citrate lyase/succinyl-CoA ligase, active site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. / Succinyl-CoA synthetase, beta subunit, conserved site ...Succinyl-CoA ligase, alpha subunit / Succinate--CoA synthetase, beta subunit / ATP-grasp fold, succinyl-CoA synthetase-type / ATP-grasp domain / Succinyl-CoA synthetase domains / ATP-citrate lyase/succinyl-CoA ligase, active site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. / Succinyl-CoA synthetase, beta subunit, conserved site / ATP-citrate lyase / succinyl-CoA ligases family signature 3. / ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / COENZYME A / Succinate--CoA ligase [ADP-forming] subunit alpha / Succinate--CoA ligase [ADP-forming] subunit beta / Succinate--CoA ligase [ADP-forming] subunit alpha
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsOsipiuk, J. / Maltseva, N. / Jedrzejczak, R. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: to be published
Title: Succinyl-CoA synthase from Francisella tularensis
Authors: Osipiuk, J. / Maltseva, N. / Jedrzejczak, R. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJun 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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: Succinate--CoA ligase [ADP-forming] subunit alpha
B: Succinate--CoA ligase [ADP-forming] subunit beta
C: Succinate--CoA ligase [ADP-forming] subunit alpha
D: Succinate--CoA ligase [ADP-forming] subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,7998
Polymers145,1424
Non-polymers1,6564
Water14,448802
1
A: Succinate--CoA ligase [ADP-forming] subunit alpha
B: Succinate--CoA ligase [ADP-forming] subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3393
Polymers72,5712
Non-polymers7681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-25 kcal/mol
Surface area25700 Å2
MethodPISA
2
C: Succinate--CoA ligase [ADP-forming] subunit alpha
D: Succinate--CoA ligase [ADP-forming] subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4605
Polymers72,5712
Non-polymers8893
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-22 kcal/mol
Surface area25860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.073, 158.735, 73.017
Angle α, β, γ (deg.)90.000, 113.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Succinate--CoA ligase [ADP-forming] subunit ... , 2 types, 4 molecules ACBD

#1: Protein Succinate--CoA ligase [ADP-forming] subunit alpha / Succinyl-CoA synthetase subunit alpha / SCS-alpha


Mass: 30950.594 Da / Num. of mol.: 2 / Mutation: A85V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: sucD, BZ14_337 / Plasmid: PMCSG92 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A454XSD0, UniProt: Q5NHF4*PLUS, succinate-CoA ligase (ADP-forming)
#2: Protein Succinate--CoA ligase [ADP-forming] subunit beta / Succinyl-CoA synthetase subunit beta / SCS-beta


Mass: 41620.633 Da / Num. of mol.: 2 / Mutation: A69T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: sucC, FTT_0504c / Plasmid: pMCSG92 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q5NHF3, succinate-CoA ligase (ADP-forming)

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Non-polymers , 4 types, 806 molecules

#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 802 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.77 Å3/Da / Density % sol: 55.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M ammonium acetate, 0.1 M bis-tris 5.5, 17% polyethylene glycol 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Aug 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.76→49.65 Å / Num. obs: 138572 / % possible obs: 97.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.047 / Rrim(I) all: 0.088 / Χ2: 1.114 / Net I/av σ(I): 18.6 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.76-1.792.50.5081.4860790.6740.3910.6460.48686.9
1.79-1.822.90.43366110.8030.3050.5340.49792.6
1.82-1.863.30.38569840.8590.2470.4590.53998.9
1.86-1.93.40.31569490.9060.1990.3740.5899.1
1.9-1.943.40.27569780.9150.1740.3260.65998.9
1.94-1.983.40.23569930.9340.1490.2790.70499.1
1.98-2.033.40.20469840.9480.130.2430.81398.4
2.03-2.093.30.18268970.9490.1170.2170.9298.1
2.09-2.153.20.15869390.9630.1030.1890.96397.9
2.15-2.223.50.14370130.9710.0890.1691.07899.4
2.22-2.33.50.13370200.9730.0830.1571.13399.1
2.3-2.393.40.12169910.9770.0760.1431.22699
2.39-2.53.40.11169580.9770.070.1321.31298.8
2.5-2.633.20.09969120.980.0640.1191.41297.5
2.63-2.793.50.09370660.9830.0580.111.49399.6
2.79-3.013.50.08570410.9850.0530.11.59299.4
3.01-3.313.30.07469640.9880.0470.0871.68898.3
3.31-3.793.50.06270400.9920.0380.0731.73699.3
3.79-4.783.40.05170700.9940.0320.061.59699.5
4.78-49.653.40.0470830.9970.0250.0471.28698.5

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MGG

6mgg


Resolution: 1.76→49.65 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.096 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.11
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 6906 5 %RANDOM
Rwork0.1857 ---
obs0.1873 131628 97.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.78 Å2 / Biso mean: 32.992 Å2 / Biso min: 14.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å2-0 Å20.48 Å2
2---0.28 Å2-0 Å2
3----0.75 Å2
Refinement stepCycle: final / Resolution: 1.76→49.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9341 0 104 802 10247
Biso mean--24.9 38.36 -
Num. residues----1250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0139730
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179403
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.63913191
X-RAY DIFFRACTIONr_angle_other_deg1.361.57721893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56351282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28224.323421
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53151703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0631533
X-RAY DIFFRACTIONr_chiral_restr0.0760.21304
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210860
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021777
LS refinement shellResolution: 1.763→1.809 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 440 -
Rwork0.271 8450 -
all-8890 -
obs--85.01 %
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)
10.10010.1078-0.14930.61790.08460.5481-0.0025-0.04750.0097-0.00160.0120.0007-0.03320.0632-0.00950.07340.01520.0020.05780.00250.0066-13.1699-0.261131.9284
20.5473-0.20360.07710.4430.26680.2673-0.0222-0.04930.06720.03570.0457-0.04420.04470.0703-0.02350.02360.0467-0.0050.15220.00010.01514.2869-2.687518.2268
30.9357-0.3837-0.03920.61880.22060.12530.0399-0.1471-0.0499-0.00120.0207-0.05090.00260.045-0.06060.059-0.0380.00490.1229-0.03050.033322.500354.283510.2055
40.54040.17770.11470.9582-0.06930.45180.1-0.1211-0.10830.0633-0.0683-0.02650.03710.0046-0.03180.0962-0.04070.00010.03830.01170.03887.293133.3406-6.1026
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 500
2X-RAY DIFFRACTION2B1 - 385
3X-RAY DIFFRACTION3C2 - 500
4X-RAY DIFFRACTION4D1 - 502

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