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- PDB-1yco: Crystal structure of a branched-chain phosphotransacylase from En... -

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Basic information

Entry
Database: PDB / ID: 1yco
TitleCrystal structure of a branched-chain phosphotransacylase from Enterococcus faecalis V583
Componentsbranched-chain phosphotransacylase
KeywordsTRANSFERASE / Structural Genomics / Protein Structure Initiative / PSI / T1914 / PTB / branched-chain phosphotransacylase / NYSGXRC / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


acyltransferase activity
Similarity search - Function
Branched-chain phosphotransacylase / Phosphate acetyl/butyryltransferase / : / Phosphate acetyl/butaryl transferase / Phosphate acetyl/butaryl transferase / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Branched-chain phosphotransacylase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsRajashankar, K.R. / Kniewel, R. / Lee, K. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a branched-chain phosphotransacylase from Enterococcus faecalis V583
Authors: Rajashankar, K.R. / Kniewel, R. / Lee, K. / Lima, C.D.
History
DepositionDec 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details ..._audit_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 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: branched-chain phosphotransacylase
B: branched-chain phosphotransacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1124
Polymers60,9222
Non-polymers1902
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-41 kcal/mol
Surface area23320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.165, 61.165, 317.995
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein branched-chain phosphotransacylase


Mass: 30461.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: ptb / Plasmid: PET T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834, DE3 / References: UniProt: Q834I9
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.41 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18.8% PEG 8000, 0.05M Potassium Phosphate Monobasic, 5% Ethylene Glycol, pH 7., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTAM Q315 / Detector: CCD / Date: Nov 6, 2004
Details: Vertical focussing mirror down stream of monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 44872 / Num. obs: 44872 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.8 Å2 / Rsym value: 0.066 / Net I/σ(I): 31.7
Reflection shellResolution: 2.4→2.49 Å / Num. unique all: 4471 / Rsym value: 0.395 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD
Starting model: Model built based on a solvent flattened experimental electron density map

Resolution: 2.4→39.75 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 274376.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residues 92 to 97 and residue 158 of protomer B are not observed in the electron density map. They are assumed to be dis-ordered. Part of the C-terminal His tag are observed, namely, ...Details: Residues 92 to 97 and residue 158 of protomer B are not observed in the electron density map. They are assumed to be dis-ordered. Part of the C-terminal His tag are observed, namely, residues 274-276 in protomer A and residue 274 in protomer B
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2171 5 %RANDOM
Rwork0.232 ---
obs0.2321 43208 96.1 %-
all-43208 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.2401 Å2 / ksol: 0.33674 e/Å3
Displacement parametersBiso mean: 45.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.84 Å20 Å20 Å2
2--3.84 Å20 Å2
3----7.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→39.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4132 0 10 172 4314
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.472
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.272.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.391 337 5 %
Rwork0.29 6397 -
obs--89.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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