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- PDB-6ewr: Putative sugar aminotransferase Spr1654 from Streptococcus pneumo... -

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Basic information

Entry
Database: PDB / ID: 6ewr
TitlePutative sugar aminotransferase Spr1654 from Streptococcus pneumoniae, PMP-form
ComponentsPutative capsular polysaccharide biosynthesis protein
KeywordsSUGAR BINDING PROTEIN / teichoic acid / pneumococcus / sugar aminotransferase / PMP
Function / homology
Function and homology information


polysaccharide biosynthetic process / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Putative capsular polysaccharide biosynthesis protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAchour, A. / Sun, R. / Sandalova, T. / Han, X.
CitationJournal: Open Biol / Year: 2018
Title: Structural and functional studies of Spr1654: an essential aminotransferase in teichoic acid biosynthesis inStreptococcus pneumoniae.
Authors: Han, X. / Sun, R. / Sandalova, T. / Achour, A.
History
DepositionNov 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative capsular polysaccharide biosynthesis protein
B: Putative capsular polysaccharide biosynthesis protein
C: Putative capsular polysaccharide biosynthesis protein
D: Putative capsular polysaccharide biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,2748
Polymers191,2814
Non-polymers9934
Water3,729207
1
A: Putative capsular polysaccharide biosynthesis protein
B: Putative capsular polysaccharide biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1374
Polymers95,6412
Non-polymers4962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-35 kcal/mol
Surface area28180 Å2
MethodPISA
2
C: Putative capsular polysaccharide biosynthesis protein
D: Putative capsular polysaccharide biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1374
Polymers95,6412
Non-polymers4962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-36 kcal/mol
Surface area28320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.899, 99.562, 108.095
Angle α, β, γ (deg.)90.00, 97.53, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A5 - 402
2010B5 - 402
1020A5 - 403
2020C5 - 403
1030A5 - 403
2030D5 - 403
1040B5 - 404
2040C5 - 404
1050B5 - 404
2050D5 - 404
1060C4 - 408
2060D4 - 408

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Putative capsular polysaccharide biosynthesis protein


Mass: 47820.371 Da / Num. of mol.: 4 / Mutation: none
Source method: isolated from a genetically manipulated source
Details: PMP
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: SP_1837 / Plasmid: pET23B / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: A0A0H2URM1
#2: Chemical
ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H13N2O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Sodium acetate trihydrate 0.1 M Sodium cacodylate trihydrate pH 6.5 30% w/v Polyethylene glycol 8 000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.4→29.8 Å / Num. obs: 64471 / % possible obs: 99 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 7.4
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2 / Num. unique obs: 6344

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LC3

4lc3


Resolution: 2.4→29.8 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.838 / SU B: 12.562 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 0.667 / ESU R Free: 0.32 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.285 3127 4.9 %RANDOM
Rwork0.242 ---
obs0.245 64471 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.972 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å21.15 Å2
2---2.42 Å20 Å2
3---3.51 Å2
Refinement stepCycle: 1 / Resolution: 2.4→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12533 0 64 207 12804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01912861
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211998
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.9717479
X-RAY DIFFRACTIONr_angle_other_deg0.969327876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48551586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4424.479547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86152220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5891560
X-RAY DIFFRACTIONr_chiral_restr0.0820.22023
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114086
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022510
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_it1.4252.4646362
X-RAY DIFFRACTIONr_mcbond_other1.4252.4646361
X-RAY DIFFRACTIONr_mcangle_it2.2963.6927942
X-RAY DIFFRACTIONr_mcangle_other2.2963.6927943
X-RAY DIFFRACTIONr_scbond_it1.442.6186499
X-RAY DIFFRACTIONr_scbond_other1.442.6186500
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3523.8619538
X-RAY DIFFRACTIONr_long_range_B_refined3.71729.03714472
X-RAY DIFFRACTIONr_long_range_B_other3.71329.03914470
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A266240.06
12B266240.06
21A260720.07
22C260720.07
31A261180.06
32D261180.06
41B262300.06
42C262300.06
51B261280.06
52D261280.06
61C267840.05
62D267840.05
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 233 -
Rwork0.323 4439 -
obs--98.73 %

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