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- PDB-3ca8: Crystal structure of Escherichia coli YdcF, an S-adenosyl-L-methi... -

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Basic information

Entry
Database: PDB / ID: 3ca8
TitleCrystal structure of Escherichia coli YdcF, an S-adenosyl-L-methionine utilizing enzyme
ComponentsProtein ydcF
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / two domains / alpha/beta fold / helix bundle / Structure 2 Function Project / S2F
Function / homology
Function and homology information


YdcF fold / YdcF like domain / Domain of unknown function DUF218 / : / DUF218 domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...YdcF fold / YdcF like domain / Domain of unknown function DUF218 / : / DUF218 domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLim, K. / Chao, K. / Lehmann, C. / Herzberg, O. / Structure 2 Function Project (S2F)
CitationJournal: Proteins / Year: 2008
Title: The Escherichia coli YdcF binds S-adenosyl-L-methionine and adopts an alpha/beta-fold characteristic of nucleotide-utilizing enzymes.
Authors: Chao, K.L. / Lim, K. / Lehmann, C. / Doseeva, V. / Howard, A.J. / Schwarz, F.P. / Herzberg, O.
History
DepositionFeb 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein ydcF
B: Protein ydcF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,89424
Polymers59,4712
Non-polymers2,42322
Water13,025723
1
A: Protein ydcF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,94712
Polymers29,7361
Non-polymers1,21111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein ydcF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,94712
Polymers29,7361
Non-polymers1,21111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.795, 39.710, 122.645
Angle α, β, γ (deg.)90.00, 96.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein ydcF


Mass: 29735.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ydcF, b1414, JW1411 / Plasmid: pET100/D-TOPO / Production host: Escherichia coli (E. coli) / References: UniProt: P34209
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 723 / 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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes, 1.7 M Ammonium sulfate, 4 % MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 1, 2005 / Details: Mirrors
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 54189 / Num. obs: 54189 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.3
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 2.8 / % possible all: 93.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXDphasing
SOLVEphasing
RESOLVEmodel building
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT
Starting model: Structure solved by MAD from the data collected in R3 space group, then molecular replacement using that model for the native single wavelength data collected in P21 space group

Resolution: 1.8→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Program CNS has also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.238 4159 -RANDOM
Rwork0.195 ---
all-54139 --
obs-54139 93 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4090 0 152 723 4965
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.017
X-RAY DIFFRACTIONr_angle_refined_deg1.6

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