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- PDB-6mel: Succinyl-CoA synthase from Campylobacter jejuni -

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Basic information

Entry
Database: PDB / ID: 6mel
TitleSuccinyl-CoA synthase from Campylobacter jejuni
Components
  • Succinate--CoA ligase [ADP-forming] subunit beta
  • Succinate--CoA ligase subunit alpha
KeywordsLIGASE / Succinyl-CoA synthase / structural genomics / CPX_90676_90715 / IDP90715 / IDP90676 / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / tricarboxylic acid cycle / nucleotide binding / magnesium ion binding / ATP binding
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 / 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
CITRIC ACID / : / Succinate--CoA ligase [ADP-forming] subunit alpha / Succinate--CoA ligase [ADP-forming] subunit beta
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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 Campylobacter jejuni
Authors: Osipiuk, J. / Maltseva, N. / Jedrzejczak, R. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 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 / 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 subunit alpha
B: Succinate--CoA ligase [ADP-forming] subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8834
Polymers72,6552
Non-polymers2282
Water8,269459
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-36 kcal/mol
Surface area27340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.072, 123.072, 146.788
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Succinate--CoA ligase subunit alpha


Mass: 30851.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: DDV82_04720, DDV86_02895 / Plasmid: pMCSG92 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A2U0Q9D2, UniProt: Q0PAY2*PLUS
#2: Protein Succinate--CoA ligase [ADP-forming] subunit beta / Succinyl-CoA synthetase subunit beta / SCS-beta


Mass: 41803.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (strain RM1221) (Campylobacter)
Strain: RM1221 / Gene: sucC, CJE0637 / Plasmid: pMCSG92 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5HVN3, succinate-CoA ligase (ADP-forming)
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 4.42 Å3/Da / Density % sol: 72.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.0 M sodium citrate, 0.1 M cacodylate buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 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: 2.06→50 Å / Num. obs: 80196 / % possible obs: 100 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.035 / Rrim(I) all: 0.11 / Χ2: 1.435 / Net I/av σ(I): 28.4 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.06-2.18.10.9491.839600.670.3521.0140.74299.9
2.1-2.139.80.78939540.8130.2630.8320.682100
2.13-2.17100.6739900.8620.2220.7070.722100
2.17-2.22100.5839530.8990.1920.6110.761100
2.22-2.279.90.51439550.9130.1720.5420.86100
2.27-2.329.90.42839830.9350.1430.4520.873100
2.32-2.389.60.36539940.9510.1240.3860.956100
2.38-2.448.90.32639390.9540.1150.3461.014100
2.44-2.5110.30.28640160.9690.0930.3011.129100
2.51-2.610.20.2539820.9770.0820.2631.294100
2.6-2.6910.20.21939710.980.0720.2311.47100
2.69-2.8100.18940100.9830.0630.1991.588100
2.8-2.929.60.16739860.9840.0570.1771.843100
2.92-3.089.50.15240110.9850.0520.162.10699.9
3.08-3.2710.30.13440000.990.0440.1412.309100
3.27-3.5210.20.11940380.9920.0390.1262.4100
3.52-3.889.50.10340380.9930.0350.1092.284100
3.88-4.4410.20.08640580.9960.0280.0912.041100
4.44-5.599.80.07141030.9970.0240.0751.777100
5.59-509.40.04842550.9990.0170.0511.59199.8

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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: 2.06→48.9 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 5.087 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.099
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1753 4010 5 %RANDOM
Rwork0.1497 ---
obs0.151 76144 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 111.01 Å2 / Biso mean: 46.019 Å2 / Biso min: 30.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.15 Å20 Å2
2--0.31 Å2-0 Å2
3----0.99 Å2
Refinement stepCycle: final / Resolution: 2.06→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5031 0 14 459 5504
Biso mean--42.62 52.22 -
Num. residues----675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0145210
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175065
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.6477041
X-RAY DIFFRACTIONr_angle_other_deg1.0041.64611847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9535701
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51525.238210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15315968
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1021512
X-RAY DIFFRACTIONr_chiral_restr0.0750.2715
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025835
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02889
LS refinement shellResolution: 2.056→2.109 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 254 -
Rwork0.246 5562 -
all-5816 -
obs--99.03 %
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)
10.2423-0.22110.11750.4503-0.08320.3602-0.014-0.00640.0647-0.027-0.0462-0.05120.00460.06190.06020.01460.01380.0030.02770.00490.026631.846979.0779-19.7102
20.2191-0.0071-0.01640.0734-0.0940.4504-0.0392-0.01820.0074-0.0268-0.02070.00720.0538-0.01330.060.02310.00360.00080.02-0.0140.01697.881866.6328-10.429
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 601
2X-RAY DIFFRACTION2B1 - 501

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