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- PDB-1pt7: Crystal structure of the apo-form of the yfdW gene product of E. coli -

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Basic information

Entry
Database: PDB / ID: 1pt7
TitleCrystal structure of the apo-form of the yfdW gene product of E. coli
ComponentsHypothetical protein yfdWHypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / CoA transferase / oxalate / acetyl-CoA / E. coli
Function / homology
Function and homology information


formyl-CoA transferase / formyl-CoA transferase activity / oxalate catabolic process / cellular response to acidic pH
Similarity search - Function
Formyl-CoA:oxalate CoA-transferase / formyl-coa transferase, domain 3 / Crotonobetainyl-coa:carnitine coa-transferase; domain 1 / CoA-transferase family III domain 3 superfamily / formyl-coa transferase, domain 3 / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III / Rossmann fold / 2-Layer Sandwich ...Formyl-CoA:oxalate CoA-transferase / formyl-coa transferase, domain 3 / Crotonobetainyl-coa:carnitine coa-transferase; domain 1 / CoA-transferase family III domain 3 superfamily / formyl-coa transferase, domain 3 / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Formyl-CoA:oxalate CoA-transferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Shigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsGruez, A. / Roig-Zamboni, V. / Valencia, C. / Campanacci, V. / Cambillau, C.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The crystal structure of the Escherichia coli yfdW gene product reveals a New fold of two interlaced rings identifying a wide family of CoA transferases.
Authors: Gruez, A. / Roig-Zamboni, V. / Valencia, C. / Campanacci, V. / Cambillau, C.
History
DepositionJun 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein yfdW
B: Hypothetical protein yfdW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,77012
Polymers96,8262
Non-polymers94410
Water9,728540
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14950 Å2
ΔGint-169 kcal/mol
Surface area28290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.921, 118.634, 136.305
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 Hypothetical protein yfdW / Hypothesis


Mass: 48412.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli, Shigella flexneri / Genus: Escherichia, Shigella / Species: , / Strain: K12, K12 / Gene: YFDW OR B2374 OR SF2441 / Plasmid: pDest17 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3)pLysS / References: UniProt: P69902
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: Ammonium phosphate, sodium hepes, pH 7.5, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
111 mg/mlprotein1drop
25 mMsodium HEPES1drop
3150 mM1dropNaCl
40.9 Mammonium phosphate1reservoir
50.1 Msodium HEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 10, 2002 / Details: Mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 85290 / Num. obs: 85290 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rsym value: 0.048 / Net I/σ(I): 9.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.268 / % possible all: 97.2
Reflection
*PLUS
Highest resolution: 1.8 Å / % possible obs: 96.7 % / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.89 Å / % possible obs: 96.7 %

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.402 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.109 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19084 2468 3 %RANDOM
Rwork0.15889 ---
all0.1598 85290 --
obs0.15985 80019 89.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.157 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å20 Å20 Å2
2---0.15 Å20 Å2
3----1.9 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6432 0 52 540 7024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0216543
X-RAY DIFFRACTIONr_bond_other_d0.0020.025830
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.9568891
X-RAY DIFFRACTIONr_angle_other_deg0.916313592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.265826
X-RAY DIFFRACTIONr_chiral_restr0.1140.2973
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027316
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021254
X-RAY DIFFRACTIONr_nbd_refined0.2240.21524
X-RAY DIFFRACTIONr_nbd_other0.2490.27153
X-RAY DIFFRACTIONr_nbtor_other0.0880.23667
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2420
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1710.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5320.214
X-RAY DIFFRACTIONr_mcbond_it1.0281.54116
X-RAY DIFFRACTIONr_mcangle_it1.70226610
X-RAY DIFFRACTIONr_scbond_it2.83632427
X-RAY DIFFRACTIONr_scangle_it4.254.52281
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.228 131
Rwork0.182 4561
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)
10.064-0.02520.01730.0243-0.0540.1842-0.01890.00810.00690.00140.0196-0.0131-0.0024-0.0104-0.00070.0098-0.0061-0.00670.006-0.00080.023316.9771-0.409126.8934
20.05670.0096-0.02220.027-0.03440.1807-0.0211-0.0052-0.00870.01150.0137-0.0127-0.0051-0.00520.00750.0134-0.0064-0.00280.0035-0.00160.02216.80120.402336.7755
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 41623 - 437
2X-RAY DIFFRACTION2BB2 - 41623 - 437
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.191 / Rfactor Rwork: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.47

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