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- PDB-4r9v: Crystal structure of sialyltransferase from photobacterium damsel... -

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Basic information

Entry
Database: PDB / ID: 4r9v
TitleCrystal structure of sialyltransferase from photobacterium damselae, residues 113-497 corresponding to the gt-b domain
ComponentsSialyltransferase 0160
KeywordsTRANSFERASE / Rossmann Fold / glycosyltransferase GT-B structural group
Function / homology
Function and homology information


negative regulation of phosphate metabolic process / phosphate ion transport / intracellular phosphate ion homeostasis / glycosyltransferase activity / metal ion binding
Similarity search - Function
Phosphate transport system protein PhoU / PhoU domain / PhoU domain / PhoU-like domain superfamily / Sialyltransferase, C-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase, N-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase PMO188 / Sialyltransferase, N-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase PMO188 / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Phosphate transport system protein PhoU / PhoU domain / PhoU domain / PhoU-like domain superfamily / Sialyltransferase, C-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase, N-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase PMO188 / Sialyltransferase, N-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase PMO188 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sialyltransferase 0160
Similarity search - Component
Biological speciesPhotobacterium damselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, Y. / Huynh, N. / Chen, X. / Fisher, A.J.
CitationJournal: Febs Lett. / Year: 2014
Title: Crystal structures of sialyltransferase from Photobacterium damselae.
Authors: Huynh, N. / Li, Y. / Yu, H. / Huang, S. / Lau, K. / Chen, X. / Fisher, A.J.
History
DepositionSep 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sialyltransferase 0160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1963
Polymers46,1151
Non-polymers802
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.444, 56.523, 87.375
Angle α, β, γ (deg.)90.00, 119.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1213-

HOH

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Components

#1: Protein Sialyltransferase 0160


Mass: 46115.492 Da / Num. of mol.: 1 / Fragment: UNP residues 113-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium damselae (bacteria) / Gene: BAA25316, bst / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66375
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8
Details: 20% (w/v) PEG-1000, 100mM imidazole, pH 8.0, 200mM Calcium Acetate, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97607 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 10, 2008 / Details: Si crystal
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97607 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 17873 / Num. obs: 17873 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 43.7 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 16.9
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1287 / % possible all: 99.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Z4T

2z4t


Resolution: 2.3→41.35 Å / SU ML: 0.31 / σ(F): 0 / Phase error: 26.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2482 1647 5.08 %RANDOM
Rwork0.1837 ---
obs0.187 17873 92.27 %-
all-32413 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine analyzeLuzzati sigma a obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.3→41.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3099 0 2 126 3227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083178
X-RAY DIFFRACTIONf_angle_d1.0754331
X-RAY DIFFRACTIONf_dihedral_angle_d14.2161154
X-RAY DIFFRACTIONf_chiral_restr0.041478
X-RAY DIFFRACTIONf_plane_restr0.005561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36770.31261270.25362502X-RAY DIFFRACTION90
2.3677-2.44410.30511390.23912497X-RAY DIFFRACTION91
2.4441-2.53150.2881290.22662525X-RAY DIFFRACTION91
2.5315-2.63280.30341280.21932560X-RAY DIFFRACTION92
2.6328-2.75260.27161350.22462563X-RAY DIFFRACTION92
2.7526-2.89770.32191520.22512540X-RAY DIFFRACTION92
2.8977-3.07920.27981440.21132584X-RAY DIFFRACTION93
3.0792-3.31680.29391280.20132558X-RAY DIFFRACTION93
3.3168-3.65050.28431350.18772617X-RAY DIFFRACTION93
3.6505-4.17820.22461540.15252577X-RAY DIFFRACTION93
4.1782-5.26240.17911290.13862586X-RAY DIFFRACTION93
5.2624-41.35710.19791470.16522657X-RAY DIFFRACTION95
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)
11.679-0.6758-0.02951.155-0.00561.3175-0.0224-0.0490.20660.15270.1286-0.1998-0.13970.3055-0.08590.2757-0.0312-0.01660.2478-0.02660.2746-28.8922-15.9265108.3111
21.0164-0.2461-0.01490.83111.10632.21420.03870.20120.1243-0.1419-0.02360.1854-0.2256-0.3505-0.00530.28940.02-0.03410.26530.05050.2842-48.0316-14.0138101.9682
31.9113-0.9972-0.64431.44871.14781.8314-0.14580.4244-0.33890.0831-0.058-0.13210.38040.08870.00130.3295-0.03510.04870.3925-0.13040.3341-28.3987-38.346589.1546
43.2263-0.29780.21421.49720.49961.3051-0.3331-0.1708-0.80590.1809-0.16230.0679-0.0233-0.21280.34790.3621-0.08530.05440.5876-0.15020.3974-46.4739-37.413187.6365
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 112:206 )A112 - 206
2X-RAY DIFFRACTION2( CHAIN A AND RESID 207:313 )A207 - 313
3X-RAY DIFFRACTION3( CHAIN A AND RESID 314:443 )A314 - 443
4X-RAY DIFFRACTION4( CHAIN A AND RESID 444:497 )A444 - 497

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