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- PDB-1q7e: Crystal Structure of YfdW protein from E. coli -

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Basic information

Entry
Database: PDB / ID: 1q7e
TitleCrystal Structure of YfdW protein from E. coli
ComponentsHypothetical protein yfdWHypothesis
KeywordsTRANSFERASE / structural genomics / intertwined dimer / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
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
METHIONINE / Formyl-CoA:oxalate CoA-transferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsGogos, A. / Gorman, J. / Shapiro, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of Escherichia coli YfdW, a type III CoA transferase.
Authors: Gogos, A. / Gorman, J. / Shapiro, L.
History
DepositionAug 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn ...audit_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE Residues Ser2 and Leu3 arise from a cloning artifact that results in a 2 amino acid ... SEQUENCE Residues Ser2 and Leu3 arise from a cloning artifact that results in a 2 amino acid insertion. Residue numbers after this insertion are equal to 2 plus the correct residue number

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein yfdW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,78410
Polymers47,6581
Non-polymers1,1269
Water6,521362
1
A: Hypothetical protein yfdW
hetero molecules

A: Hypothetical protein yfdW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,56820
Polymers95,3172
Non-polymers2,25118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area16570 Å2
ΔGint-247 kcal/mol
Surface area28980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.366, 69.605, 73.219
Angle α, β, γ (deg.)90.00, 108.63, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer generated by: xyz(1) = -1.0000*x+ 0.0000*y+ 0.0000*z+ 92.3658 xyz(2) = 0.0000*x+ 1.0000*y+ 0.0000*z+ -0.0016 xyz(3) = 0.0000*x+ 0.0000*y+ -1.0000*z+ 0.0004

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Components

#1: Protein Hypothetical protein yfdW / Hypothesis


Mass: 47658.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YFDW / Production host: Escherichia coli (E. coli) / References: UniProt: P69902
#2: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 3

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.3447.41
2
3
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, hanging drop6.570% MPD, 0.1 M Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
2982vapor diffusion, hanging drop6.570% MPD, 0.1 M Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
2983vapor diffusion, hanging drop6.570% MPD, 0.1 M Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X9A10.9793
SYNCHROTRONAPS 31-ID20.9793
SYNCHROTRONAPS 31-ID30.9793
Detector
TypeIDDetectorDate
MARRESEARCH1CCDMay 23, 2003
MARRESEARCH2CCDJan 1, 2003
MARRESEARCH3CCDJan 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 56025 / Num. obs: 56025 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Rsym value: 0.098 / Net I/σ(I): 11.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4 / Num. unique all: 5451 / Rsym value: 0.295 / % possible all: 95.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMAC5refinement
RefinementMethod to determine structure: SAD / Resolution: 1.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.186 2723 -random
Rwork0.156 ---
obs-53302 97.3 %-
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3156 0 65 362 3583
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.012
X-RAY DIFFRACTIONr_angle_refined_deg1.4

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