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- PDB-1xk7: Crystal Structure- C2 form- of Escherichia coli Crotonobetainyl-C... -

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Basic information

Entry
Database: PDB / ID: 1xk7
TitleCrystal Structure- C2 form- of Escherichia coli Crotonobetainyl-CoA: carnitine CoA transferase (CaiB)
ComponentsCrotonobetainyl-CoA:carnitine CoA-transferase
KeywordsTRANSFERASE / CaiB / CoA transferase / Carnitine / Crotonobetainyl coA / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics
Function / homology
Function and homology information


L-carnitine CoA-transferase / L-carnitine CoA-transferase activity / carnitine catabolic process / cytoplasm
Similarity search - Function
L-carnitine CoA-transferase CaiB / : / formyl-coa transferase, domain 3 / Crotonobetainyl-coa:carnitine coa-transferase; domain 1 / formyl-coa transferase, domain 3 / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III domain 3 superfamily / CoA-transferase family III / Rossmann fold ...L-carnitine CoA-transferase CaiB / : / formyl-coa transferase, domain 3 / Crotonobetainyl-coa:carnitine coa-transferase; domain 1 / formyl-coa transferase, domain 3 / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III domain 3 superfamily / CoA-transferase family III / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-carnitine CoA-transferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRangarajan, E.S. / Li, Y. / Iannuzzi, P. / Cygler, M. / Matte, A. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Biochemistry / Year: 2005
Title: Crystal Structure of Escherichia coli Crotonobetainyl-CoA: Carnitine CoA-Transferase (CaiB) and Its Complexes with CoA and Carnitinyl-CoA.
Authors: Rangarajan, E.S. / Li, Y. / Iannuzzi, P. / Cygler, M. / Matte, A.
History
DepositionSep 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 13, 2013Group: Structure summary
Revision 1.4Aug 23, 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_special_symmetry / struct_conn / struct_ref_seq_dif
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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Crotonobetainyl-CoA:carnitine CoA-transferase
B: Crotonobetainyl-CoA:carnitine CoA-transferase
C: Crotonobetainyl-CoA:carnitine CoA-transferase


Theoretical massNumber of molelcules
Total (without water)138,7503
Polymers138,7503
Non-polymers00
Water21,1501174
1
A: Crotonobetainyl-CoA:carnitine CoA-transferase

A: Crotonobetainyl-CoA:carnitine CoA-transferase


Theoretical massNumber of molelcules
Total (without water)92,5002
Polymers92,5002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
2
B: Crotonobetainyl-CoA:carnitine CoA-transferase
C: Crotonobetainyl-CoA:carnitine CoA-transferase


Theoretical massNumber of molelcules
Total (without water)92,5002
Polymers92,5002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11960 Å2
ΔGint-85 kcal/mol
Surface area30050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.276, 106.167, 69.676
Angle α, β, γ (deg.)90.00, 107.45, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-421-

HOH

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Components

#1: Protein Crotonobetainyl-CoA:carnitine CoA-transferase


Mass: 46250.043 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: caiB / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): E. coli. DL41 (DE3)
References: UniProt: P31572, Transferases; Transferring sulfur-containing groups; CoA-transferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1174 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.5
Details: 12.5% (w/v) PEG 8000, 0.1 M Tris-Cl (pH 7.5), 0.2 M MgCl2, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 16, 2004 / Details: Mirrors
RadiationMonochromator: Silicone / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 217938 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 18.6 Å2 / Rsym value: 0.083 / Net I/σ(I): 12.6
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 4.59 / Num. unique all: 16757 / Rsym value: 0.401 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XK6

1xk6


Resolution: 1.6→45.44 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 4357195.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 8476 5 %RANDOM
Rwork0.187 ---
obs-167996 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.0382 Å2 / ksol: 0.360035 e/Å3
Displacement parametersBiso mean: 19.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å2-0.36 Å20 Å2
2--0.48 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→45.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9561 0 0 1174 10735
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d1.29
X-RAY DIFFRACTIONc_mcbond_it0.471.5
X-RAY DIFFRACTIONc_mcangle_it0.782
X-RAY DIFFRACTIONc_scbond_it1.32
X-RAY DIFFRACTIONc_scangle_it1.692.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.254 1436 5.1 %
Rwork0.237 26535 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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