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- PDB-2nu9: C123aT Mutant of E. coli Succinyl-CoA Synthetase Orthorhombic Cry... -

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Basic information

Entry
Database: PDB / ID: 2nu9
TitleC123aT Mutant of E. coli Succinyl-CoA Synthetase Orthorhombic Crystal Form
Components
  • Succinyl-CoA ligase [ADP-forming] subunit alpha
  • Succinyl-CoA synthetase beta chain
KeywordsLIGASE / citric acid cycle / heterotetramer / ATP-GRASP fold / Rossmann fold
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 / cytoplasm / 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 beta / Succinate--CoA ligase [ADP-forming] subunit alpha
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFraser, M.E.
CitationJournal: ACTA CRYSTALLOGR.,SECT.D / Year: 2007
Title: Participation of Cys 123alpha of Escherichia coli Succinyl-CoA Synthetase in Catalysis
Authors: Hidber, E. / Brownie, E.R. / Hayakawa, K. / Fraser, M.E.
History
DepositionNov 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Succinyl-CoA ligase [ADP-forming] subunit alpha
B: Succinyl-CoA synthetase beta chain
D: Succinyl-CoA ligase [ADP-forming] subunit alpha
E: Succinyl-CoA synthetase beta chain
F: Succinyl-CoA ligase [ADP-forming] subunit alpha
G: Succinyl-CoA synthetase beta chain
H: Succinyl-CoA ligase [ADP-forming] subunit alpha
I: Succinyl-CoA synthetase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)288,61720
Polymers284,7798
Non-polymers3,83912
Water724
1
A: Succinyl-CoA ligase [ADP-forming] subunit alpha
B: Succinyl-CoA synthetase beta chain
F: Succinyl-CoA ligase [ADP-forming] subunit alpha
G: Succinyl-CoA synthetase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,30910
Polymers142,3894
Non-polymers1,9196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12940 Å2
ΔGint-128 kcal/mol
Surface area49450 Å2
MethodPISA
2
D: Succinyl-CoA ligase [ADP-forming] subunit alpha
E: Succinyl-CoA synthetase beta chain
H: Succinyl-CoA ligase [ADP-forming] subunit alpha
I: Succinyl-CoA synthetase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,30910
Polymers142,3894
Non-polymers1,9196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12900 Å2
ΔGint-127 kcal/mol
Surface area49450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.530, 154.900, 240.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 29756.174 Da / Num. of mol.: 4 / Mutation: C123T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sucD / Plasmid: pGS202 / Production host: Escherichia coli (E. coli) / Strain (production host): TK3D18
References: UniProt: P0AGE9, succinate-CoA ligase (ADP-forming)
#2: Protein
Succinyl-CoA synthetase beta chain / SCS-beta


Mass: 41438.496 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sucC / Plasmid: pGS202 / Production host: Escherichia coli (E. coli) / Strain (production host): TK3D18
References: UniProt: P0A836, succinate-CoA ligase (ADP-forming)
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.22 Å3/Da / Density % sol: 61.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: BICINE, ammonium sulfate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9504
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 2, 2002 / Details: monochromator
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9504 Å / Relative weight: 1
ReflectionResolution: 2.9→200 Å / Num. all: 81001 / Num. obs: 81001 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 56.8 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 12.2
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3360 / % possible all: 83.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2SCU

2scu


Resolution: 2.9→20.11 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4125 -random
Rwork0.229 ---
all0.23 80943 --
obs0.23 80943 98.3 %-
Displacement parametersBiso mean: 38.22 Å2
Baniso -1Baniso -2Baniso -3
1--12.87 Å20 Å20 Å2
2--9.49 Å20 Å2
3---3.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.9→20.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19804 0 232 4 20040
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 2.9→3.03 Å / Rfactor Rfree error: 0.016
RfactorNum. reflection% reflection
Rfree0.356 491 -
Rwork0.339 --
obs-9371 92.5 %

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