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- PDB-6blg: Crystal Structure of Sugar Transaminase from Klebsiella pneumonia... -

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Basic information

Entry
Database: PDB / ID: 6blg
TitleCrystal Structure of Sugar Transaminase from Klebsiella pneumoniae Complexed with PLP
ComponentsdTDP-4-amino-4,6-dideoxygalactose transaminase
KeywordsTRANSFERASE / pyridoxal phosphate (PLP)-dependent sugar aminotransferase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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 / pyridoxal phosphate 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
FORMIC ACID / dTDP-4-amino-4,6-dideoxygalactose transaminase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsMaltseva, N. / Kim, Y. / Shatsman, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health United States
CitationJournal: To Be Published
Title: Crystal Structure of Sugar Transaminase from Klebsiella pneumoniae Complexed with PLP
Authors: Maltseva, N. / Kim, Y. / Shatsman, S. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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 1.3Nov 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: dTDP-4-amino-4,6-dideoxygalactose transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,78814
Polymers42,7561
Non-polymers1,03213
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: dTDP-4-amino-4,6-dideoxygalactose transaminase
hetero molecules

A: dTDP-4-amino-4,6-dideoxygalactose transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,57528
Polymers85,5112
Non-polymers2,06426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area8320 Å2
ΔGint-232 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.853, 130.853, 138.752
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-405-

SO4

21A-406-

SO4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein dTDP-4-amino-4,6-dideoxygalactose transaminase


Mass: 42755.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578) (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: wecE, KPN_04291 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 gold
References: UniProt: A6TGH9, dTDP-4-amino-4,6-dideoxygalactose transaminase

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Non-polymers , 6 types, 65 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.67 Å3/Da / Density % sol: 53.99 % / Description: cube
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6M Ammonium sulfate, 0.1M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 10, 2017 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→37.77 Å / Num. obs: 26700 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 48.07 Å2 / CC1/2: 0.748 / Rsym value: 0.07 / Net I/σ(I): 18.3
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1324 / Rsym value: 0.894 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZAH

4zah


Resolution: 2.102→37.767 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 24.02
RfactorNum. reflection% reflection
Rfree0.2253 1364 5.11 %
Rwork0.1748 --
obs0.1774 26689 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 53.4 Å2
Refinement stepCycle: LAST / Resolution: 2.102→37.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2981 0 55 52 3088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063129
X-RAY DIFFRACTIONf_angle_d0.7494245
X-RAY DIFFRACTIONf_dihedral_angle_d19.921855
X-RAY DIFFRACTIONf_chiral_restr0.048461
X-RAY DIFFRACTIONf_plane_restr0.005544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1017-2.17680.32771270.26222489X-RAY DIFFRACTION99
2.1768-2.2640.27871300.22542525X-RAY DIFFRACTION100
2.264-2.3670.29141380.21462496X-RAY DIFFRACTION100
2.367-2.49180.22271260.19552521X-RAY DIFFRACTION100
2.4918-2.64790.22721370.2012519X-RAY DIFFRACTION100
2.6479-2.85220.28131450.20942522X-RAY DIFFRACTION100
2.8522-3.13920.27181500.21362523X-RAY DIFFRACTION100
3.1392-3.59310.26321330.19712536X-RAY DIFFRACTION100
3.5931-4.52570.20671500.14172549X-RAY DIFFRACTION100
4.5257-37.77310.16581280.14622645X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.1268-2.1503-4.50961.37430.23833.2492-0.43920.0973-0.42-0.03250.22090.04470.80790.1510.29660.6487-0.0083-0.03630.4008-0.06380.46826.649721.2168-2.4112
25.90210.83770.7553.5668-4.40435.9415-0.29850.5315-0.2092-0.60940.0508-0.03450.7346-0.07080.2160.48430.02010.0470.4844-0.0810.28639.963430.702-15.1098
31.7401-0.28490.21071.28970.78721.9592-0.03920.14750.4669-0.09130.0813-0.0008-0.2786-0.0114-0.03620.4265-0.0140.02890.32660.04690.418610.823753.331-5.967
42.3735-1.6368-0.94740.70620.24181.18540.03750.2376-0.0143-0.028-0.00970.00270.02130.1855-0.00050.4442-0.0248-0.03230.4311-0.02270.347812.718437.9611-11.0479
56.02711.70783.60321.64140.79824.90260.30440.51560.3592-0.5138-0.10750.116-0.22350.7195-0.1360.66590.0741-0.01280.483-0.00890.426429.035233.4932-13.3124
66.4706-4.7882-2.20034.59471.44921.52910.17820.2614-0.3712-0.2027-0.18460.26780.0918-0.13080.03680.4629-0.03660.01420.3542-0.01950.4233-6.939833.4388-4.2198
73.66251.2758-0.54032.583-0.66615.07870.17330.1690.3706-0.0775-0.09960.231-0.4999-0.2498-0.06770.40320.02390.02680.3958-0.01770.5034-10.165847.81270.8083
83.65453.6171-2.3324.0538-1.4765.5897-0.0834-0.52380.38750.1808-0.13950.3-0.0721-0.16030.29090.37410.03910.05070.3709-0.02560.3467-4.719645.128614.501
95.28952.46150.46594.1790.05280.850.0473-0.35770.5408-0.08640.00410.4909-0.1992-0.0701-0.05470.42690.02640.05730.3451-0.01650.3298-5.144846.72747.3939
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 54 )
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 152 )
4X-RAY DIFFRACTION4chain 'A' and (resid 153 through 217 )
5X-RAY DIFFRACTION5chain 'A' and (resid 218 through 236 )
6X-RAY DIFFRACTION6chain 'A' and (resid 237 through 273 )
7X-RAY DIFFRACTION7chain 'A' and (resid 274 through 299 )
8X-RAY DIFFRACTION8chain 'A' and (resid 300 through 327 )
9X-RAY DIFFRACTION9chain 'A' and (resid 328 through 376 )

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