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- PDB-4hl6: YfdE from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 4hl6
TitleYfdE from Escherichia coli
ComponentsUncharacterized protein YfdE
KeywordsTRANSFERASE
Function / homology
Function and homology information


CoA:oxalate CoA-transferase / acetyl-CoA:oxalate CoA-transferase / CoA-transferase activity / protein homodimerization activity
Similarity search - Function
: / 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 ...: / 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
Acetyl-CoA:oxalate CoA-transferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsMullins, E.A. / Sullivan, K.L. / Nyffeler, K.E. / Kappock, T.J.
CitationJournal: Plos One / Year: 2013
Title: Function and X-Ray crystal structure of Escherichia coli YfdE.
Authors: Mullins, E.A. / Sullivan, K.L. / Kappock, T.J.
History
DepositionOct 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Aug 21, 2013Group: Database references
Revision 1.3Mar 26, 2014Group: Structure summary
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software
Revision 1.5Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein YfdE
B: Uncharacterized protein YfdE
C: Uncharacterized protein YfdE
D: Uncharacterized protein YfdE
E: Uncharacterized protein YfdE
F: Uncharacterized protein YfdE


Theoretical massNumber of molelcules
Total (without water)263,3046
Polymers263,3046
Non-polymers00
Water18,3931021
1
A: Uncharacterized protein YfdE
B: Uncharacterized protein YfdE


Theoretical massNumber of molelcules
Total (without water)87,7682
Polymers87,7682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10310 Å2
ΔGint-98 kcal/mol
Surface area27560 Å2
MethodPISA
2
C: Uncharacterized protein YfdE
D: Uncharacterized protein YfdE


Theoretical massNumber of molelcules
Total (without water)87,7682
Polymers87,7682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-99 kcal/mol
Surface area27660 Å2
MethodPISA
3
E: Uncharacterized protein YfdE
F: Uncharacterized protein YfdE


Theoretical massNumber of molelcules
Total (without water)87,7682
Polymers87,7682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10190 Å2
ΔGint-97 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.422, 79.527, 276.189
Angle α, β, γ (deg.)90.000, 99.950, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Uncharacterized protein YfdE


Mass: 43883.980 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yfdE, b2371, JW2368 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P76518
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1021 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% (w/v) PEG-8000, 0.1 M Tris-HCl, 0.2 M magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 27, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. obs: 107843 / % possible obs: 79.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Χ2: 1.334 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
2.12-2.163.10.5062.249560.5060.85873.7
2.16-2.23.10.4472.549970.4470.86574
2.2-2.243.10.3942.849460.3940.89674
2.24-2.283.10.3373.349400.3370.90173
2.28-2.333.10.2983.650000.2980.89675.3
2.33-2.393.10.2654.150610.2650.92575
2.39-2.453.10.2344.849770.2340.95973.3
2.45-2.513.10.2045.749610.2040.99674.4
2.51-2.593.10.196.149820.191.07374.1
2.59-2.673.10.1597.749970.1591.15174.2
2.67-2.773.10.151849870.1511.273.9
2.77-2.883.10.12510.449930.1251.25974
2.88-3.0130.10312.951180.1031.38175.9
3.01-3.1730.08915.552400.0891.41177.8
3.17-3.3730.0818.753940.081.73679.6
3.37-3.6230.06823.357270.0681.94584.2
3.62-3.9930.06127.362050.0612.21991.3
3.99-4.573.30.05232.766130.0522.16897.4
4.57-5.753.70.04332.668190.0431.62899.9
5.75-503.70.03541.269300.0351.35499.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ed9

4ed9


Resolution: 2.12→42.479 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8151 / SU ML: 0.29 / σ(F): 0 / Phase error: 25.73 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 5455 5.06 %Random
Rwork0.1885 ---
obs0.191 107822 79.72 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.435 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 88.32 Å2 / Biso mean: 32.8256 Å2 / Biso min: 12.36 Å2
Baniso -1Baniso -2Baniso -3
1-14.8518 Å2-0 Å2-1.215 Å2
2---7.3098 Å20 Å2
3----7.542 Å2
Refinement stepCycle: LAST / Resolution: 2.12→42.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17260 0 0 1021 18281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317650
X-RAY DIFFRACTIONf_angle_d0.7723940
X-RAY DIFFRACTIONf_chiral_restr0.0542657
X-RAY DIFFRACTIONf_plane_restr0.0033153
X-RAY DIFFRACTIONf_dihedral_angle_d13.9516542
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.12-2.14350.3031700.232430643234323471
2.1435-2.16870.33851410.230531533294329475
2.1687-2.19510.31451990.236531543353335373
2.1951-2.22290.29551550.226431343289328974
2.2229-2.25220.26151770.208131173294329474
2.2522-2.2830.28791690.222831363305330573
2.283-2.31560.31461640.219831653329332975
2.3156-2.35020.31251660.231232293395339575
2.3502-2.38690.30971610.224531863347334776
2.3869-2.42610.29251690.22331473316331673
2.4261-2.46790.30621740.208431513325332575
2.4679-2.51280.251660.210931423308330874
2.5128-2.56110.24841640.213731643328332874
2.5611-2.61330.27471830.207431483331333174
2.6133-2.67020.26431670.19931543321332174
2.6702-2.73230.27821530.223331733326332673
2.7323-2.80060.28071500.227731993349334975
2.8006-2.87630.25511580.217231493307330774
2.8763-2.96090.25141720.211332513423342375
2.9609-3.05640.27721870.20932723459345977
3.0564-3.16570.27071770.214233133490349078
3.1657-3.29240.24951930.201733973590359079
3.2924-3.44210.25361830.195734953678367882
3.4421-3.62350.20722020.176836483850385085
3.6235-3.85040.21412120.167738324044404490
3.8504-4.14750.17832200.169240804300430095
4.1475-4.56440.19922270.149342634490449098
4.5644-5.22390.18322270.1508429945264526100
5.2239-6.57760.22152290.1769434545744574100
6.5776-42.48720.18792400.156944074647464799

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