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- PDB-1psw: Structure of E. coli ADP-heptose lps heptosyltransferase II -

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Basic information

Entry
Database: PDB / ID: 1psw
TitleStructure of E. coli ADP-heptose lps heptosyltransferase II
ComponentsADP-HEPTOSE LPS HEPTOSYLTRANSFERASE II
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / T832 / NYSGXRC / LPS BIOSYNTHETIC PATHWAY / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


ADP-heptose-lipopolysaccharide heptosyltransferase activity / Transferases / lipopolysaccharide core region biosynthetic process / cytosol
Similarity search - Function
ADP-heptose--LPS heptosyltransferase 2 / Glycosyl transferase, family 9 / Glycosyltransferase family 9 (heptosyltransferase) / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADP-heptose--LPS heptosyltransferase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKniewel, R. / Buglino, J. / Solorzano, V. / Wu, J. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Structure of E. coli ADP-heptose lps heptosyltransferase II
Authors: Kniewel, R. / Buglino, J. / Solorzano, V. / Wu, J. / Lima, C.D.
History
DepositionJun 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-HEPTOSE LPS HEPTOSYLTRANSFERASE II


Theoretical massNumber of molelcules
Total (without water)39,6181
Polymers39,6181
Non-polymers00
Water5,098283
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.407, 150.125, 49.674
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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Components

#1: Protein ADP-HEPTOSE LPS HEPTOSYLTRANSFERASE II / E.C.2.4.99.- / lipopolysaccharide core biosynthesis / lipopolysaccharide heptosyltransferase II rfaF / rfaF


Mass: 39617.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rfaF / Plasmid: PET T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 DE3 / References: UniProt: P37692, EC: 2.4.99.-
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.91 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.6
Details: 1M Ammonium Phospate, 0.1M, Na Citrate pH 5.6 , VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9798 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 7, 2003
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 37604 / Num. obs: 37529 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.093
Reflection shellResolution: 1.9→1.97 Å / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
CNS1.1refinement
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→19.96 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1537 5 %RANDOM
Rwork0.201 ---
obs0.2011 30596 93 %-
all-32899 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.3843 Å2 / ksol: 0.381507 e/Å3
Displacement parametersBiso mean: 29 Å2
Baniso -1Baniso -2Baniso -3
1--2.4 Å20 Å20 Å2
2--2.54 Å20 Å2
3----0.14 Å2
Refine analyzeLuzzati coordinate error free: 0.24 Å / Luzzati sigma a free: 0.14 Å
Refinement stepCycle: LAST / Resolution: 2→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 0 283 2901
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it2.752
X-RAY DIFFRACTIONc_scangle_it3.762.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.233 206 4.7 %
Rwork0.207 4172 -
obs--81.3 %
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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