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- PDB-1pqy: Crystal structure of formyl-coA transferase yfdW from E. coli -

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Basic information

Entry
Database: PDB / ID: 1pqy
TitleCrystal structure of formyl-coA transferase yfdW from E. coli
ComponentsHypothetical protein yfdWHypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / 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
Formyl-CoA:oxalate CoA-transferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 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
DepositionJun 19, 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 / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 999SEQUENCE 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


Theoretical massNumber of molelcules
Total (without water)47,7521
Polymers47,7521
Non-polymers00
Water4,684260
1
A: Hypothetical protein yfdW

A: Hypothetical protein yfdW


Theoretical massNumber of molelcules
Total (without water)95,5042
Polymers95,5042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area12310 Å2
ΔGint-88 kcal/mol
Surface area29710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.261, 69.539, 73.109
Angle α, β, γ (deg.)90.00, 108.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hypothetical protein yfdW / Hypothesis


Mass: 47752.227 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, calcium chloride, 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
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X9B10.9793
SYNCHROTRONAPS 31-ID20.9793
Detector
TypeIDDetectorDate
MARRESEARCH1CCDMay 23, 2003
MARRESEARCH2CCDJun 3, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SiSINGLE WAVELENGTHMx-ray1
2DiamondSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.35→27.99 Å / Num. all: 18133 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 23.8 Å2 / Limit h max: 37 / Limit h min: -39 / Limit k max: 29 / Limit k min: -39 / Limit l max: 31 / Limit l min: 0 / Observed criterion F max: 1432802.39 / Observed criterion F min: 5.6 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 24.3
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 7 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 20 / Rsym value: 0.18 / % possible all: 97.8

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→27.99 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 877 4.9 %random
Rwork0.177 ---
all-18396 --
obs-18078 98.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 46.0103 Å2 / ksol: 0.359186 e/Å3
Displacement parametersBiso max: 57.06 Å2 / Biso mean: 20.98 Å2 / Biso min: 5.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20.16 Å2
2--2.48 Å20 Å2
3----1.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.13 Å
Luzzati d res high-2.35
Refinement stepCycle: LAST / Resolution: 2.35→27.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3163 0 0 260 3423
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg23.4
X-RAY DIFFRACTIONx_torsion_impr_deg0.89
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.35-2.460.2861215.40.20721260.0262300224797.7
2.46-2.590.2241195.30.17321230.0212281224298.3
2.59-2.750.233944.20.17821610.0242290225598.5
2.75-2.960.207833.70.16921510.0232270223498.4
2.96-3.260.2271004.40.17221790.0232312227998.6
3.26-3.730.21165.20.16821310.0192278224798.6
3.73-4.690.1761155.10.1521400.0162313225597.5
4.69-27.990.2041295.60.21121900.0182365231998.1
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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