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

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Basic information

Entry
Database: PDB / ID: 6ewq
TitlePutative sugar aminotransferase Spr1654 from Streptococcus pneumoniae, PLP-form
ComponentsPutative capsular polysaccharide biosynthesis protein
KeywordsSUGAR BINDING PROTEIN / teichoic acid / pneumococcus / sugar aminotransferase / PLP
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
PYRIDOXAL-5'-PHOSPHATE / Putative capsular polysaccharide biosynthesis protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)192,2708
Polymers191,2814
Non-polymers9894
Water14,718817
1
A: Putative capsular polysaccharide biosynthesis protein
B: Putative capsular polysaccharide biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1354
Polymers95,6412
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-35 kcal/mol
Surface area27930 Å2
MethodPISA
2
C: Putative capsular polysaccharide biosynthesis protein
D: Putative capsular polysaccharide biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1354
Polymers95,6412
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-35 kcal/mol
Surface area28120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.008, 99.324, 107.608
Angle α, β, γ (deg.)90.00, 97.74, 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:

Component-ID: _ / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRAA4 - 40410 - 410
21THRTHRBB4 - 40410 - 410
12LEULEUAA4 - 40310 - 409
22LEULEUCC4 - 40310 - 409
13THRTHRAA4 - 40410 - 410
23THRTHRDD4 - 40410 - 410
14THRTHRBB4 - 40410 - 410
24THRTHRCC4 - 40410 - 410
15LEULEUBB4 - 40310 - 409
25LEULEUDD4 - 40310 - 409
16THRTHRCC4 - 40410 - 410
26THRTHRDD4 - 40410 - 410

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: PLP
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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 817 / 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: 2.19 Å3/Da / Density % sol: 43.76 %
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: 2.2→29.7 Å / Num. obs: 79389 / % possible obs: 95 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 6.4
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2 / Num. unique obs: 7743

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LC3

4lc3


Resolution: 2.2→29.7 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.834 / SU B: 10.072 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.422 / ESU R Free: 0.277 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.288 3866 4.9 %RANDOM
Rwork0.238 ---
obs0.241 79389 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å2-0 Å20.19 Å2
2---1.95 Å2-0 Å2
3---3.14 Å2
Refinement stepCycle: 1 / Resolution: 2.2→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12506 0 60 817 13383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01912833
X-RAY DIFFRACTIONr_bond_other_d0.0070.0212180
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.9717448
X-RAY DIFFRACTIONr_angle_other_deg1.203328117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68951580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43224.463549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.968152197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9531560
X-RAY DIFFRACTIONr_chiral_restr0.0870.22019
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02114250
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022770
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_it1.8292.3216347
X-RAY DIFFRACTIONr_mcbond_other1.8282.3216346
X-RAY DIFFRACTIONr_mcangle_it2.8873.4737918
X-RAY DIFFRACTIONr_mcangle_other2.8873.4737919
X-RAY DIFFRACTIONr_scbond_it2.0142.5276486
X-RAY DIFFRACTIONr_scbond_other2.0142.5276487
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1653.719531
X-RAY DIFFRACTIONr_long_range_B_refined5.21219.115476
X-RAY DIFFRACTIONr_long_range_B_other5.11219.02215233
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 / Rms dev position: 0.03 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A51452
12B51452
21A52480
22C52480
31A51374
32D51374
41B51490
42C51490
51B51430
52D51430
61C51346
62D51346
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 257 -
Rwork0.314 5493 -
obs--92.8 %

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