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- PDB-5z8b: Truncated N-acetylglucosaminyl transferase KfiA from E. coli K5 s... -

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Basic information

Entry
Database: PDB / ID: 5z8b
TitleTruncated N-acetylglucosaminyl transferase KfiA from E. coli K5 strain apo form
ComponentsKfiA protein
KeywordsTRANSFERASE / Glycosyltransferase
Function / homologyNucleotide-diphospho-sugar transferases / KfiA protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsHori, H. / Kakuta, Y.
CitationJournal: To Be Published
Title: Crysta structure of N-acetylglucosaminyl transferase KfiA from E. coli K5 strain
Authors: Hori, H. / Kakuta, Y.
History
DepositionJan 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KfiA protein
B: KfiA protein


Theoretical massNumber of molelcules
Total (without water)55,5502
Polymers55,5502
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint0 kcal/mol
Surface area21160 Å2
2
A: KfiA protein

B: KfiA protein


Theoretical massNumber of molelcules
Total (without water)55,5502
Polymers55,5502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area2480 Å2
ΔGint-12 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.409, 70.862, 147.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein KfiA protein


Mass: 27774.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: KfiA, kfiA, A4T40_20310, A9X62_20115, APT94_25675, CCL28_04130, CT143_12180, CT144_09435, CUB98_02030, CUB99_17445, SM09_03227
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q47332
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.81 Å3/Da / Density % sol: 31.88 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.91→73.71 Å / Num. obs: 16958 / % possible obs: 99.5 % / Redundancy: 3.8 % / Net I/σ(I): 8.9
Reflection shellResolution: 2.91→3.08 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→73.71 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.872 / SU B: 22.191 / SU ML: 0.402 / Cross valid method: THROUGHOUT / ESU R Free: 0.485 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26517 471 5 %RANDOM
Rwork0.17777 ---
obs0.18227 8885 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.122 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2--1.88 Å2-0 Å2
3----2.37 Å2
Refinement stepCycle: 1 / Resolution: 2.91→73.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 0 40 3370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193419
X-RAY DIFFRACTIONr_bond_other_d0.0020.023261
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.9634618
X-RAY DIFFRACTIONr_angle_other_deg0.9937525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1965415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7524.606165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.43115613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1261518
X-RAY DIFFRACTIONr_chiral_restr0.0870.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213855
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02789
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9183.4131660
X-RAY DIFFRACTIONr_mcbond_other1.93.411659
X-RAY DIFFRACTIONr_mcangle_it3.1925.1152072
X-RAY DIFFRACTIONr_mcangle_other3.1935.1192073
X-RAY DIFFRACTIONr_scbond_it2.1333.6311759
X-RAY DIFFRACTIONr_scbond_other2.1333.6341760
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5635.3352546
X-RAY DIFFRACTIONr_long_range_B_refined5.60339.0013706
X-RAY DIFFRACTIONr_long_range_B_other5.60439.0223703
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.912→2.988 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 32 -
Rwork0.273 647 -
obs--99.85 %

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