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- PDB-6mgg: Succinyl-CoA synthase from Francisella tularensis, phosphorylated... -

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Basic information

Entry
Database: PDB / ID: 6mgg
TitleSuccinyl-CoA synthase from Francisella tularensis, phosphorylated, in complex with CoA
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 (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / tricarboxylic acid cycle / nucleotide binding / magnesium ion binding / ATP binding ...succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / tricarboxylic acid cycle / nucleotide binding / magnesium ion binding / ATP binding / metal ion binding / cytosol
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, subdomain 1 / ATP-grasp fold, B domain / 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
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: 1.78 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
DepositionSep 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: 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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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: 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)147,13212
Polymers145,3004
Non-polymers1,8328
Water19,3841076
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)73,5666
Polymers72,6502
Non-polymers9164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-30 kcal/mol
Surface area27310 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)73,5666
Polymers72,6502
Non-polymers9164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-31 kcal/mol
Surface area26830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.911, 158.338, 73.585
Angle α, β, γ (deg.)90.000, 111.730, 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: 31029.562 Da / Num. of mol.: 2 / Mutation: A85V, H247NEP
Source method: isolated from a genetically manipulated source
Details: H247 is phosphorylated
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) / Strain (production host): BL21(DE3)
References: UniProt: A0A0G2RQ73, 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, 1084 molecules

#3: Chemical ChemComp-COA / COENZYME A


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1076 / 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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M magnesium chloride, 0.1 M Tris buffer, 16% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 25, 2018
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.78→38.18 Å / Num. obs: 134691 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.04 / Rrim(I) all: 0.078 / Χ2: 1.439 / Net I/av σ(I): 23.6 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.813.20.7121.7967010.5990.4760.8591.193100
1.81-1.843.40.61567660.6770.3960.7331.257100
1.84-1.883.70.53766960.7650.3260.6291.276100
1.88-1.923.80.44767280.8430.2670.5211.327100
1.92-1.963.80.35867140.8810.2130.4181.327100
1.96-23.80.28967110.9220.1720.3361.36100
2-2.053.80.23767020.9440.1410.2761.4100
2.05-2.113.80.20167450.9610.1190.2341.424100
2.11-2.173.80.16567250.9720.0980.1921.411100
2.17-2.243.80.14367230.9780.0850.1671.452100
2.24-2.323.80.12967570.9830.0770.151.435100
2.32-2.423.80.11366660.9870.0670.1311.456100
2.42-2.533.80.09767760.990.0570.1131.459100
2.53-2.663.80.08566980.9920.0510.0991.493100
2.66-2.833.80.06767520.9950.040.0781.512100
2.83-3.043.80.05667650.9960.0330.0651.53100
3.04-3.353.80.04367340.9980.0250.051.571100
3.35-3.833.80.03567380.9980.0210.041.582100
3.83-4.833.80.03267750.9980.0190.0371.555100
4.83-38.183.70.0468190.9960.0250.0471.6699.6

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JKJ

1jkj


Resolution: 1.78→38.18 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.323 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.116
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 6633 4.9 %RANDOM
Rwork0.1765 ---
obs0.1784 128013 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 85.31 Å2 / Biso mean: 26.803 Å2 / Biso min: 12.04 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å2-0.19 Å2
2---0.68 Å20 Å2
3----0.46 Å2
Refinement stepCycle: final / Resolution: 1.78→38.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10037 0 114 1077 11228
Biso mean--27.23 34.82 -
Num. residues----1345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01410446
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179976
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.66714168
X-RAY DIFFRACTIONr_angle_other_deg0.9831.65223336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14751384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92224.647439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.061151835
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.91534
X-RAY DIFFRACTIONr_chiral_restr0.0760.21401
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211707
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021765
LS refinement shellResolution: 1.782→1.828 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 444 -
Rwork0.272 9069 -
all-9513 -
obs--95.45 %
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)
10.2027-0.2041-0.06090.4562-0.06960.2339-0.0001-0.0464-0.0110.0233-0.0717-0.0463-0.0210.07710.07190.0276-0.025-0.01450.11550.02910.078822.781753.70239.4155
20.1210.0642-0.04630.044-0.03060.50470.013-0.029-0.0572-0.009-0.0291-0.03660.0367-0.0140.01610.0581-0.0093-0.01260.05810.01320.10478.130633.1107-2.495
30.1799-0.0245-0.10950.48960.1330.2092-0.0278-0.0210.0240.02720.03620.00310.00720.0243-0.00840.05250.0060.00480.0744-0.00060.07-12.97450.067732.4115
40.047-0.108-0.07540.29060.11440.3271-0.0036-0.01960.04760.00770.029-0.0972-0.01170.1577-0.02550.0017-0.0087-0.0110.1638-0.00930.120114.002-0.128121.4464
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 502
2X-RAY DIFFRACTION2B1 - 502
3X-RAY DIFFRACTION3C2 - 502
4X-RAY DIFFRACTION4D1 - 502

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