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- PDB-3ufx: Thermus aquaticus succinyl-CoA synthetase in complex with GDP-Mn2+ -

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Basic information

Entry
Database: PDB / ID: 3ufx
TitleThermus aquaticus succinyl-CoA synthetase in complex with GDP-Mn2+
Components
  • Succinyl-CoA synthetase beta subunit
  • succinyl-CoA synthetase alpha subunit
KeywordsLIGASE / ATP-grasp fold
Function / homology
Function and homology information


succinate-CoA ligase (GDP-forming) / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / tricarboxylic acid cycle / nucleotide binding / GTP binding / magnesium ion binding ...succinate-CoA ligase (GDP-forming) / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / tricarboxylic acid cycle / nucleotide binding / GTP binding / magnesium ion binding / ATP 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
GUANOSINE-5'-DIPHOSPHATE / : / Succinate--CoA ligase [GDP-forming] subunit alpha / Succinate--CoA ligase [GDP-forming] subunit beta
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsFraser, M.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Biochemical and structural characterization of the GTP-preferring succinyl-CoA synthetase from Thermus aquaticus.
Authors: Joyce, M.A. / Hayakawa, K. / Wolodko, W.T. / Fraser, M.E.
History
DepositionNov 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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 / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: succinyl-CoA synthetase alpha subunit
B: Succinyl-CoA synthetase beta subunit
D: succinyl-CoA synthetase alpha subunit
E: Succinyl-CoA synthetase beta subunit
F: succinyl-CoA synthetase alpha subunit
G: Succinyl-CoA synthetase beta subunit
H: succinyl-CoA synthetase alpha subunit
I: Succinyl-CoA synthetase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,68516
Polymers294,6938
Non-polymers1,9938
Water13,241735
1
A: succinyl-CoA synthetase alpha subunit
B: Succinyl-CoA synthetase beta subunit
D: succinyl-CoA synthetase alpha subunit
E: Succinyl-CoA synthetase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,3438
Polymers147,3464
Non-polymers9964
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: succinyl-CoA synthetase alpha subunit
G: Succinyl-CoA synthetase beta subunit
H: succinyl-CoA synthetase alpha subunit
I: Succinyl-CoA synthetase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,3438
Polymers147,3464
Non-polymers9964
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: succinyl-CoA synthetase alpha subunit
B: Succinyl-CoA synthetase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1714
Polymers73,6732
Non-polymers4982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-36 kcal/mol
Surface area25860 Å2
MethodPISA
4
D: succinyl-CoA synthetase alpha subunit
E: Succinyl-CoA synthetase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1714
Polymers73,6732
Non-polymers4982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-35 kcal/mol
Surface area25800 Å2
MethodPISA
5
F: succinyl-CoA synthetase alpha subunit
G: Succinyl-CoA synthetase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1714
Polymers73,6732
Non-polymers4982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-35 kcal/mol
Surface area25720 Å2
MethodPISA
6
H: succinyl-CoA synthetase alpha subunit
I: Succinyl-CoA synthetase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1714
Polymers73,6732
Non-polymers4982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-35 kcal/mol
Surface area25830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)261.700, 126.800, 110.600
Angle α, β, γ (deg.)90.000, 112.760, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
succinyl-CoA synthetase alpha subunit / succinyl-CoA ligase alpha subunit


Mass: 30755.527 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P09143*PLUS, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases
#2: Protein
Succinyl-CoA synthetase beta subunit / succinyl-CoA ligase beta subunit


Mass: 42917.609 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P25126*PLUS, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / 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: 2.87 Å3/Da / Density % sol: 57.16 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 10% PEG3350, 100 mM MES, 200 mM potassium chloride, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 19, 2005
RadiationMonochromator: Kohzu double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.35→200 Å / Num. all: 120106 / Num. obs: 120106 / % possible obs: 86.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.129 / Χ2: 1.514 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.35-2.390.41433830.505149.3
2.39-2.430.42140570.476158.6
2.43-2.480.40747080.457168.1
2.48-2.530.40852790.504177
2.53-2.590.40857780.524183.6
2.59-2.650.36260290.553187.4
2.65-2.710.32662020.64189.7
2.71-2.790.30162730.71191.3
2.79-2.870.26264100.807192.8
2.87-2.960.23264820.949193.4
2.96-3.070.19364730.987193.8
3.07-3.190.1864831.197193.9
3.19-3.330.15665121.461194.2
3.33-3.510.13665601.756195.1
3.51-3.730.12366262.048194.9
3.73-4.020.11265942.221195.5
4.02-4.420.10166232.381195.4
4.42-5.060.09566212.497194.8
5.06-6.380.09565302.058193.8
6.38-2000.0964832.555191.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.521 / Cor.coef. Fo:Fc: 0.157 / Cor.coef. Io to Ic: 0.155
Highest resolutionLowest resolution
Rotation4 Å20 Å
Translation3 Å20 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
AMoREphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1JKJ AND 1OI7

1jkj

1oi7


Resolution: 2.35→50.994 Å / Occupancy max: 1 / Occupancy min: 0.77 / FOM work R set: 0.8085 / SU ML: 0.37 / σ(F): 1.35 / Phase error: 26.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 6048 5.04 %RANDOM
Rwork0.2042 ---
all0.2075 120106 --
obs0.2062 120075 86.73 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.3 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso max: 139.1 Å2 / Biso mean: 42.4683 Å2 / Biso min: 11.05 Å2
Baniso -1Baniso -2Baniso -3
1-10.4611 Å2-0 Å27.1564 Å2
2---10.7743 Å20 Å2
3---0.3133 Å2
Refinement stepCycle: LAST / Resolution: 2.35→50.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19696 0 116 735 20547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00820131
X-RAY DIFFRACTIONf_angle_d1.04127265
X-RAY DIFFRACTIONf_chiral_restr0.0643178
X-RAY DIFFRACTIONf_plane_restr0.0043509
X-RAY DIFFRACTIONf_dihedral_angle_d13.7997469
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.37650.3355930.31972028212147
2.3765-2.40450.34861140.32282448256255
2.4045-2.43380.32951420.29762607274960
2.4338-2.46460.34561490.2992903305267
2.4646-2.4970.34081710.28643153332473
2.497-2.53120.34691810.28893424360578
2.5312-2.56740.34191820.27713631381383
2.5674-2.60570.32912040.24783714391886
2.6057-2.64640.32142070.23253872407988
2.6464-2.68980.26391910.22693915410689
2.6898-2.73620.27052280.23153908413691
2.7362-2.7860.27652120.24214009422192
2.786-2.83950.28842420.23294057429993
2.8395-2.89750.30412030.23494062426593
2.8975-2.96050.31812100.22914111432194
2.9605-3.02930.28582150.22814094430993
3.0293-3.10510.27042340.21894114434894
3.1051-3.1890.282160.23094088430494
3.189-3.28290.27832120.22734129434194
3.2829-3.38880.25132260.23444123434994
3.3888-3.50990.27542380.2124142438095
3.5099-3.65040.2242310.20474163439495
3.6504-3.81650.22062130.18684218443196
3.8165-4.01760.20192120.16784185439795
4.0176-4.26920.18362070.15514220442795
4.2692-4.59860.18912180.13054170438895
4.5986-5.0610.16842200.14024203442395
5.061-5.79250.21112290.17694129435894
5.7925-7.29450.24782010.22214146434793
7.2945-51.0060.21092470.20424061430891

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