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- PDB-1xvv: Crystal Structure of CaiB mutant D169A in complex with carnitinyl-CoA -

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Basic information

Entry
Database: PDB / ID: 1xvv
TitleCrystal Structure of CaiB mutant D169A in complex with carnitinyl-CoA
ComponentsCrotonobetainyl-CoA:carnitine CoA-transferase
KeywordsTRANSFERASE / CaiB / CoA-transferase / Carnityl-CoA / Asp mutant
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-CARNITINYL-COA INNER SALT / L-carnitine CoA-transferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRangarajan, E.S. / Li, Y. / Iannuzzi, P. / Cygler, M. / Matte, A.
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
DepositionOct 28, 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: Advisory / Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Crotonobetainyl-CoA:carnitine CoA-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3202
Polymers45,4091
Non-polymers9111
Water1,47782
1
A: Crotonobetainyl-CoA:carnitine CoA-transferase
hetero molecules

A: Crotonobetainyl-CoA:carnitine CoA-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6394
Polymers90,8182
Non-polymers1,8212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area16600 Å2
ΔGint-75 kcal/mol
Surface area26800 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.627, 86.627, 163.863
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 45408.828 Da / Num. of mol.: 1 / Mutation: D169A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: caiB / Plasmid: pGEX-4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P31572, Transferases; Transferring sulfur-containing groups; CoA-transferases
#2: Chemical ChemComp-CCQ / L-CARNITINYL-COA INNER SALT / O5'-(4-(3-{2-[2-((R)-3-HYDROXY-4-(TRIMETHYLAMMONIO)-1-OXO-BUTYL)SULFANYL-ETHYLCARBAMOYL]-ETHYLCARBAMOYL}-(R)-3-HYDROXY-2,2-DIMETHYL-PROPYL)-1-HYDROXY-3-OXIDO-1,3-DIOXO-2,4-DIOXA-1,3-DIPHOSPHABUT-1-YL) 3'-PHOSPHO-ADENOSINE


Mass: 910.718 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H49N8O18P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.59 Å3/Da / Density % sol: 65.48 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 1.35M Sodium citrate, 0.1M Tris-Cl (pH 7.0), VAPOR DIFFUSION, temperature 21K

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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: Aug 23, 2004
RadiationMonochromator: Silicone / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.22→50 Å / Num. all: 31626 / Num. obs: 31586 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Rsym value: 0.062 / Net I/σ(I): 19.4
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 5.86 / Rsym value: 0.613 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XK6

1xk6


Resolution: 2.4→49.09 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.912 / SU B: 16.755 / SU ML: 0.189 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25228 1274 5.1 %RANDOM
Rwork0.20537 ---
obs0.20772 23801 99.7 %-
all-25150 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.823 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3001 0 58 82 3141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223137
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9784277
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8445401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.23824.206126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.37915458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3831513
X-RAY DIFFRACTIONr_chiral_restr0.0880.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022407
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.21395
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22136
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2127
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.2119
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4941.52046
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.84623160
X-RAY DIFFRACTIONr_scbond_it1.42931264
X-RAY DIFFRACTIONr_scangle_it2.2894.51117
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 91 -
Rwork0.285 1716 -
obs--100 %
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)
12.6119-1.38161.21212.9175-1.26022.8261-0.146-0.5432-0.25150.51090.3930.3812-0.0037-0.7025-0.247-0.16560.03460.0316-0.10570.0791-0.226445.021449.56910.2671
26.17650.0111-2.18452.81480.65195.0057-0.16570.42260.0697-0.19760.30120.0965-0.1080.1924-0.1355-0.2515-0.07950.01770.00210.1979-0.075963.366263.7819-22.0636
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 2267 - 229
2X-RAY DIFFRACTION1AA323 - 405326 - 408
3X-RAY DIFFRACTION2AA227 - 322230 - 325

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