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- PDB-1poi: CRYSTAL STRUCTURE OF GLUTACONATE COENZYME A-TRANSFERASE FROM ACID... -

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Basic information

Entry
Database: PDB / ID: 1poi
TitleCRYSTAL STRUCTURE OF GLUTACONATE COENZYME A-TRANSFERASE FROM ACIDAMINOCOCCUS FERMENTANS TO 2.55 ANGSTOMS RESOLUTION
Components(GLUTACONATE COENZYME A-TRANSFERASE) x 2
KeywordsTRANSFERASE / COA / GLUTAMATE / PROTEIN FERMENTATION
Function / homology
Function and homology information


glutaconate CoA-transferase / glutaconate CoA-transferase activity / glutamate catabolic process via 2-hydroxyglutarate / cytoplasm
Similarity search - Function
Defensin A-like - #40 / Glutaconate Coenzyme A-transferase / Glutaconate Coenzyme A-transferase / Coenzyme A transferase family I / Coenzyme A transferase / Coenzyme A transferase / NagB/RpiA transferase-like / Defensin A-like / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Glutaconate CoA-transferase subunit A / Glutaconate CoA-transferase subunit B
Similarity search - Component
Biological speciesAcidaminococcus fermentans (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.5 Å
AuthorsJacob, U. / Mack, M. / Clausen, T. / Huber, R. / Buckel, W. / Messerschmidt, A.
CitationJournal: Structure / Year: 1997
Title: Glutaconate CoA-transferase from Acidaminococcus fermentans: the crystal structure reveals homology with other CoA-transferases.
Authors: Jacob, U. / Mack, M. / Clausen, T. / Huber, R. / Buckel, W. / Messerschmidt, A.
History
DepositionJan 24, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _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: GLUTACONATE COENZYME A-TRANSFERASE
B: GLUTACONATE COENZYME A-TRANSFERASE
C: GLUTACONATE COENZYME A-TRANSFERASE
D: GLUTACONATE COENZYME A-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,9775
Polymers127,9144
Non-polymers641
Water7,891438
1
A: GLUTACONATE COENZYME A-TRANSFERASE
B: GLUTACONATE COENZYME A-TRANSFERASE
C: GLUTACONATE COENZYME A-TRANSFERASE
D: GLUTACONATE COENZYME A-TRANSFERASE
hetero molecules

A: GLUTACONATE COENZYME A-TRANSFERASE
B: GLUTACONATE COENZYME A-TRANSFERASE
C: GLUTACONATE COENZYME A-TRANSFERASE
D: GLUTACONATE COENZYME A-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,95410
Polymers255,8278
Non-polymers1272
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area30440 Å2
ΔGint-177 kcal/mol
Surface area74220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)145.120, 152.270, 130.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-470-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.038176, -0.000853, -0.999271), (-0.001572, -0.999999, 0.000793), (-0.99927, 0.00154, -0.038178)32.71137, 58.01692, 33.84743
2given(0.03158, -0.005887, -0.999484), (-0.000552, -0.999983, 0.005873), (-0.999501, 0.000366, -0.031583)32.7498, 58.07874, 33.80648

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Components

#1: Protein GLUTACONATE COENZYME A-TRANSFERASE


Mass: 35390.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidaminococcus fermentans (bacteria) / Cellular location (production host): CYTOSOL / Production host: Escherichia coli (E. coli) / References: UniProt: Q59111
#2: Protein GLUTACONATE COENZYME A-TRANSFERASE


Mass: 28566.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidaminococcus fermentans (bacteria) / Cellular location (production host): CYTOSOL / Production host: Escherichia coli (E. coli) / References: UniProt: Q59112
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 5.5 / Details: AMMONIUM SULFATE/PEG PH=5.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 mg/mlprotein1drop
20.93 Mammonium sulfate1drop
324 mMMES1drop
40.2 mM1dropCuSO4
51 %PEG80001drop
61.65 Mammonium sulfate1reservoir
70.1 MMES1reservoir
81 mM1reservoirCuSO4
95 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→7 Å / Num. obs: 37201 / % possible obs: 83 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.098
Reflection shellResolution: 2.55→2.64 Å / % possible all: 32

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMV. 5.23data reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→7 Å / Rfactor Rwork: 0.19 / Rfactor obs: 0.19 / Cross valid method: FREE-R / σ(F): 0
Displacement parametersBiso mean: 24 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8994 0 1 438 9433
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 37201 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS

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