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- PDB-4piw: Crystal structure of sugar aminotransferase WecE from Escherichia... -

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Basic information

Entry
Database: PDB / ID: 4piw
TitleCrystal structure of sugar aminotransferase WecE from Escherichia coli K-12
ComponentsTDP-4-keto-6-deoxy-D-glucose transaminase family protein
KeywordsTRANSFERASE / sugar aminotransferase / Structural Genomics / PSI-Biology / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homology
Function and homology information


dTDP-4-amino-4,6-dideoxygalactose transaminase / dTDP-4-amino-4,6-dideoxygalactose transaminase activity / enterobacterial common antigen biosynthetic process / polysaccharide biosynthetic process / pyridoxal phosphate binding / identical protein binding
Similarity search - Function
dTDP-4-amino-4,6-dideoxygalactose transaminase WecE-like / dTDP-4-amino-4,6-dideoxygalactose transaminase WecE / DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...dTDP-4-amino-4,6-dideoxygalactose transaminase WecE-like / dTDP-4-amino-4,6-dideoxygalactose transaminase WecE / DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / dTDP-4-amino-4,6-dideoxygalactose transaminase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWang, F. / Xu, W. / Helmich, K.E. / Singh, S. / Yennamalli, R.M. / Miller, M.D. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01GM098248 United States
CitationJournal: To Be Published
Title: Crystal structure of sugar aminotransferase WecE from Escherichia coli K-12
Authors: Wang, F. / Xu, W. / Helmich, K.E. / Singh, S. / Yennamalli, R.M. / Bingman, C.A. / Miller, M.D. / Thorson, J.S. / Phillips Jr., G.N.
History
DepositionMay 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Data collection
Revision 2.0Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: entity / pdbx_audit_support ...entity / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _entity.formula_weight / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TDP-4-keto-6-deoxy-D-glucose transaminase family protein
B: TDP-4-keto-6-deoxy-D-glucose transaminase family protein
C: TDP-4-keto-6-deoxy-D-glucose transaminase family protein
D: TDP-4-keto-6-deoxy-D-glucose transaminase family protein
E: TDP-4-keto-6-deoxy-D-glucose transaminase family protein
F: TDP-4-keto-6-deoxy-D-glucose transaminase family protein
G: TDP-4-keto-6-deoxy-D-glucose transaminase family protein
H: TDP-4-keto-6-deoxy-D-glucose transaminase family protein


Theoretical massNumber of molelcules
Total (without water)359,6408
Polymers359,6408
Non-polymers00
Water5,188288
1
A: TDP-4-keto-6-deoxy-D-glucose transaminase family protein
B: TDP-4-keto-6-deoxy-D-glucose transaminase family protein


Theoretical massNumber of molelcules
Total (without water)89,9102
Polymers89,9102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-31 kcal/mol
Surface area25850 Å2
MethodPISA
2
C: TDP-4-keto-6-deoxy-D-glucose transaminase family protein
D: TDP-4-keto-6-deoxy-D-glucose transaminase family protein


Theoretical massNumber of molelcules
Total (without water)89,9102
Polymers89,9102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-32 kcal/mol
Surface area25760 Å2
MethodPISA
3
E: TDP-4-keto-6-deoxy-D-glucose transaminase family protein
F: TDP-4-keto-6-deoxy-D-glucose transaminase family protein


Theoretical massNumber of molelcules
Total (without water)89,9102
Polymers89,9102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-28 kcal/mol
Surface area25830 Å2
MethodPISA
4
G: TDP-4-keto-6-deoxy-D-glucose transaminase family protein
H: TDP-4-keto-6-deoxy-D-glucose transaminase family protein


Theoretical massNumber of molelcules
Total (without water)89,9102
Polymers89,9102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-23 kcal/mol
Surface area25990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.341, 87.483, 161.554
Angle α, β, γ (deg.)90.000, 91.100, 90.000
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
TDP-4-keto-6-deoxy-D-glucose transaminase family protein


Mass: 44955.012 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: wecE / Production host: Escherichia coli (E. coli) / References: UniProt: N2U028, UniProt: P27833*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein solution (10~25 mg/ml, 25 mM Tris or HEPES pH 7.5, 150 mM NaCl) mixed in a 1:1 ratio with the well solution (0.1 M Sodium Acetate, 0.1 M MES pH6.5, 30% (w/v) PEG 2000 MME), ...Details: Protein solution (10~25 mg/ml, 25 mM Tris or HEPES pH 7.5, 150 mM NaCl) mixed in a 1:1 ratio with the well solution (0.1 M Sodium Acetate, 0.1 M MES pH6.5, 30% (w/v) PEG 2000 MME), cryoprotected with 27% PEG 2000 MME and 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 17, 2004
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.15
ReflectionResolution: 2.7→48.8 Å / Num. all: 275071 / Num. obs: 90907 / % possible obs: 84.23 % / Redundancy: 3 % / Rmerge(I) obs: 0.1109 / Net I/σ(I): 10.31

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHENIX(phenix.refine: 1.9_1678)phasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.9_1678)refinement
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ensemble model of 1MDO, 3DR7, 3FRK, 4LC3 and 4OCA

1mdo

3dr7

3frk

4lc3

4oca


Resolution: 2.7→48.801 Å / Cross valid method: FREE R-VALUE / σ(F): 0.25 / Phase error: 34.67 / Stereochemistry target values: TWIN_LSQ_F
Details: THE ACTIVE SITE CONTENTS ARE LIKELY TO BE A MIXTURE OF NON-BOUND PLP, COVALENTLY BOUND LYSINE-PLP AND PMP. ONLY COVALENTLY BOUND LYSINE-PLP (LLP) WAS BUILT IN DUE TO THE DATA RESOLUTION LIMIT.
RfactorNum. reflection% reflection
Rfree0.2754 1709 1.97 %
Rwork0.2363 --
obs0.2372 86559 89.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.93 Å2 / Biso mean: 41.2807 Å2 / Biso min: 5.33 Å2
Refinement stepCycle: final / Resolution: 2.7→48.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22629 0 0 288 22917
Biso mean---35.38 -
Num. residues----2888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223111
X-RAY DIFFRACTIONf_angle_d0.50331341
X-RAY DIFFRACTIONf_chiral_restr0.023486
X-RAY DIFFRACTIONf_plane_restr0.0034044
X-RAY DIFFRACTIONf_dihedral_angle_d10.4458420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.78720.3211480.30038292X-RAY DIFFRACTION95
2.7872-2.88680.32441540.29068324X-RAY DIFFRACTION96
2.8868-3.00230.35651680.27828334X-RAY DIFFRACTION96
3.0023-3.13890.32031550.26488319X-RAY DIFFRACTION96
3.1389-3.30430.30981530.26598343X-RAY DIFFRACTION96
3.3043-3.51120.2881090.2545708X-RAY DIFFRACTION65
3.5112-3.78210.30361220.23166331X-RAY DIFFRACTION72
3.7821-4.16220.2911240.21636701X-RAY DIFFRACTION76
4.1622-4.76350.21571570.20318227X-RAY DIFFRACTION94
4.7635-5.99760.24051560.21388196X-RAY DIFFRACTION93
5.9976-37.69940.21661530.21468166X-RAY DIFFRACTION91

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