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- PDB-7mi0: Crystal Structure of Glycosyltransferase from Rickettsia africae ESF-5 -

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Basic information

Entry
Database: PDB / ID: 7mi0
TitleCrystal Structure of Glycosyltransferase from Rickettsia africae ESF-5
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / SSGCID / Glycosyltransferase / Rickettsia africae / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


glycosyltransferase activity
Similarity search - Function
: / Glycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesRickettsia africae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Crystal structure of acetoacetyl-CoA reductase from Rickettsia felis.
Authors: Rodarte, J.V. / Abendroth, J. / Edwards, T.E. / Lorimer, D.D. / Staker, B.L. / Zhang, S. / Myler, P.J. / McLaughlin, K.J.
History
DepositionApr 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2535
Polymers45,1111
Non-polymers1424
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.270, 111.270, 163.740
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-519-

HOH

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Components

#1: Protein Glycosyltransferase


Mass: 45111.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia africae (strain ESF-5) (bacteria)
Strain: ESF-5 / Gene: RAF_ORF0434 / Plasmid: RiafA.17295.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3PN56
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.25 Å3/Da / Density % sol: 62.2 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Rigaku Reagens JCSG+ screen, condtion E1: 1000mM sodium citrate tribasic, 100mM sodium cacodylate / HCl pH 6.5: RiafA.17295.a.B1.PW36512 at 23.9mg/ml: tray: 240851 e1: cryo: 20% EG: puck osj0-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97919 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 17, 2013 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 13909 / % possible obs: 99.8 % / Redundancy: 7.074 % / Biso Wilson estimate: 55.775 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.09 / Χ2: 0.906 / Net I/σ(I): 21.03
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.9-2.987.2490.6463.3610080.9080.696100
2.98-3.067.3150.4974.489630.9240.535100
3.06-3.157.2830.435.029570.9510.463100
3.15-3.247.2490.3366.429240.9640.362100
3.24-3.357.2180.2568.438890.9780.275100
3.35-3.477.2290.19510.768880.9850.21100
3.47-3.67.2110.13614.538330.9930.147100
3.6-3.747.1690.10717.898120.9960.116100
3.74-3.917.2130.09620.347710.9960.104100
3.91-4.17.1240.06726.167600.9980.072100
4.1-4.327.080.06228.47240.9980.067100
4.32-4.597.1060.0534.226720.9990.054100
4.59-4.96.9890.04536.336400.9990.049100
4.9-5.296.9740.04635.596130.9990.049100
5.29-5.86.9380.04534.245600.9990.049100
5.8-6.486.8060.04634.565160.9990.05100
6.48-7.496.6980.03739.894640.9990.0499.8
7.49-9.176.5590.02554.2139910.02799.5
9.17-12.976.1790.02161.0431810.02298.5
12.97-505.040.02248.571980.9990.02591.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19 4205refinement
PDB_EXTRACT3.27data extraction
MR-Rosettaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MR-rosetta starting from pdb entry 6d9t

6d9t


Resolution: 2.9→47.49 Å / SU ML: 0.335 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5914
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 1346 9.7 %0
Rwork0.1941 12524 --
obs0.1982 13870 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.67 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2876 0 4 37 2917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00372946
X-RAY DIFFRACTIONf_angle_d0.5574016
X-RAY DIFFRACTIONf_chiral_restr0.0442485
X-RAY DIFFRACTIONf_plane_restr0.0046507
X-RAY DIFFRACTIONf_dihedral_angle_d12.57041045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-30.29171360.25481221X-RAY DIFFRACTION100
3-3.120.32511230.25111220X-RAY DIFFRACTION100
3.12-3.270.33161320.27861231X-RAY DIFFRACTION100
3.27-3.440.2931310.22311217X-RAY DIFFRACTION100
3.44-3.650.22161330.1891231X-RAY DIFFRACTION100
3.65-3.940.23441300.20571243X-RAY DIFFRACTION100
3.94-4.330.22931370.1671241X-RAY DIFFRACTION99.93
4.33-4.960.20871350.14921266X-RAY DIFFRACTION100
4.96-6.240.19361380.19311282X-RAY DIFFRACTION100
6.24-47.490.22171510.18311372X-RAY DIFFRACTION99.28
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)
13.76397776599-0.20588370872-0.005979439393661.11586627896-0.9117929406587.9596010274-0.315355029953-0.2058830397430.0477691916321-0.2080611339280.03904799712460.121329133433-0.40276081511-1.219934946120.2188838413880.4820616550750.164796280132-0.1536662778680.530546751055-0.07057661640060.569263962915.340002050147.430445341973.807737158
24.37866807518-0.134233561195-0.008800742707692.98586488917-0.09270216728268.94730518695-0.1689394291690.304864092168-0.131066053178-0.605709155046-0.119092675496-0.1080043877260.05792316767770.9448376231080.2627559071150.4525486507860.0585634493421-0.03899010328820.4857532175380.0250284056630.3798484842731.758219307142.784157772969.5888618407
31.869244558230.08381418065580.9387773496024.64058338864-0.1734213001392.913969076540.227521370468-0.0762216363858-0.352022898458-0.0312842348195-0.3318513254770.4018767235020.700447431076-0.07988726930620.08350619759570.5181126781840.0363047954126-0.01134053914340.34923971939-0.05054560163340.47539996225423.757636552525.523316537193.8761702258
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: UNK / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 10 through 92 )10 - 921 - 83
22chain 'A' and (resid 93 through 171 )93 - 17184 - 162
33chain 'A' and (resid 172 through 388 )172 - 388163 - 379

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