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

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Basic information

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


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
Putative capsular polysaccharide biosynthesis protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 4, 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
D: Putative capsular polysaccharide biosynthesis protein
C: Putative capsular polysaccharide biosynthesis protein
B: Putative capsular polysaccharide biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)191,2814
Polymers191,2814
Non-polymers00
Water12,845713
1
A: Putative capsular polysaccharide biosynthesis protein
B: Putative capsular polysaccharide biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)95,6412
Polymers95,6412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-32 kcal/mol
Surface area28700 Å2
MethodPISA
2
D: Putative capsular polysaccharide biosynthesis protein
C: Putative capsular polysaccharide biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)95,6412
Polymers95,6412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-32 kcal/mol
Surface area28850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.330, 99.982, 110.422
Angle α, β, γ (deg.)90.00, 97.66, 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
1010A6 - 403
2010B6 - 403
1020A6 - 404
2020C6 - 404
1030A6 - 404
2030D6 - 404
1040B4 - 404
2040C4 - 404
1050B4 - 404
2050D4 - 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Gene: SP_1837, Spr1654 / Plasmid: pET23B / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: A0A0H2URM1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 713 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
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: ESRF / Beamline: ID30B / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 130980 / % possible obs: 97 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 10.9
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 13145

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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: 1.9→30 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.892 / SU B: 10.034 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.168 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 6467 4.9 %RANDOM
Rwork0.236 ---
obs0.238 130980 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å20.04 Å2
2---0.06 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12564 0 0 713 13277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01912829
X-RAY DIFFRACTIONr_bond_other_d0.0080.0212231
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.96517431
X-RAY DIFFRACTIONr_angle_other_deg1.371328255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33551590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.03424.481549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.769152223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4041560
X-RAY DIFFRACTIONr_chiral_restr0.0930.22027
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02114266
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022766
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_it0.6461.3866378
X-RAY DIFFRACTIONr_mcbond_other0.6461.3866377
X-RAY DIFFRACTIONr_mcangle_it1.0812.0737962
X-RAY DIFFRACTIONr_mcangle_other1.0812.0737963
X-RAY DIFFRACTIONr_scbond_it0.71.4946451
X-RAY DIFFRACTIONr_scbond_other0.71.4956452
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1462.2039470
X-RAY DIFFRACTIONr_long_range_B_refined3.88711.8615188
X-RAY DIFFRACTIONr_long_range_B_other3.79411.60814930
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)
11A511100.07
12B511100.07
21A508020.06
22C508020.06
31A503740.07
32D503740.07
41B505720.07
42C505720.07
51B506700.07
52D506700.07
61C508540.07
62D508540.07
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 507 -
Rwork0.318 9221 -
obs--98.11 %
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)
11.5755-0.51620.05881.11910.08980.4231-0.02160.03380.0708-0.0230.017-0.1425-0.05640.08160.00460.0261-0.01450.0580.0168-0.00880.203611.74680.2743.57
21.97740.5626-0.3110.95910.08870.746-0.0343-0.2186-0.05770.0656-0.0237-0.16110.08610.18360.0580.02610.0267-0.04630.06080.00470.20194.677107.85250.924
31.90730.39470.22271.1151-0.03920.5919-0.0822-0.14250.22790.02540.05380.1875-0.1306-0.09180.02830.0390.0335-0.02840.0363-0.02450.181-29.591109.56449.749
41.2454-0.3354-0.15831.3482-0.00040.4426-0.06430.0767-0.1479-0.00450.00860.33560.1423-0.07520.05570.0597-0.03010.06890.0172-0.02880.2855-22.66878.5594.498
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 404
2X-RAY DIFFRACTION2B4 - 404
3X-RAY DIFFRACTION3C4 - 408
4X-RAY DIFFRACTION4D4 - 404

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