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- PDB-6p61: Structure of a Glycosyltransferase from Leptospira borgpetersenii... -

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Basic information

Entry
Database: PDB / ID: 6p61
TitleStructure of a Glycosyltransferase from Leptospira borgpetersenii serovar Hardjo-bovis (strain JB197)
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyGlycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases / transferase activity / CITRIC ACID / Glycosyltransferase
Function and homology information
Biological speciesLeptospira borgpetersenii serovar Hardjo-bovis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of a Glycosyltransferase from Leptospira borgpetersenii serovar Hardjo-bovis (strain JB197)
Authors: Abendroth, J. / Conrady, D.G. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMay 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyltransferase
B: Glycosyltransferase
C: Glycosyltransferase
D: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,02326
Polymers106,8174
Non-polymers2,20622
Water12,863714
1
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3677
Polymers26,7041
Non-polymers6636
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0835
Polymers26,7041
Non-polymers3784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1456
Polymers26,7041
Non-polymers4405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4298
Polymers26,7041
Non-polymers7257
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.250, 123.170, 76.770
Angle α, β, γ (deg.)90.000, 92.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycosyltransferase /


Mass: 26704.361 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira borgpetersenii serovar Hardjo-bovis (strain JB197) (bacteria)
Strain: JB197 / Gene: LBJ_1113 / Plasmid: LpboA.19148.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Variant (production host): BL21(DE3) / References: UniProt: Q04TP4
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 714 / 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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Optimization screen based on MCSG-1, condition F3: 200mM Ammonium citrate dibasic pH 5.5, 18% (w/V) PEG 3350: LpboA.19148.a.B1.PS38508 at 26.29mg/ml, seeded: cryo: 20% EG: tray 309474 e3: ...Details: Optimization screen based on MCSG-1, condition F3: 200mM Ammonium citrate dibasic pH 5.5, 18% (w/V) PEG 3350: LpboA.19148.a.B1.PS38508 at 26.29mg/ml, seeded: cryo: 20% EG: tray 309474 e3: puck irc8-7. Protein purified in 20mM HEPES pH7, 300mM NaCl, 5% Glycerol, 1mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2019
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.95→33.152 Å / Num. obs: 75239 / % possible obs: 99 % / Redundancy: 3.281 % / Biso Wilson estimate: 33.519 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.061 / Χ2: 1.012 / Net I/σ(I): 14.82 / Num. measured all: 246869 / Scaling rejects: 30
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.95-22.290.3732.1611769557251400.7970.47792.2
2-2.062.7840.3252.9415032547353990.8660.40198.6
2.06-2.123.3330.264.4117701532753110.9320.3199.7
2.12-2.183.4610.2155.3917867517351630.9550.25499.8
2.18-2.253.4350.2046.0117142501049910.9550.24299.6
2.25-2.333.3210.176.8216022484248240.9690.20399.6
2.33-2.423.3280.1358.3915456465446440.980.16199.8
2.42-2.523.5060.10910.5515672447244700.9870.129100
2.52-2.633.5190.111.6815129430642990.9880.11899.8
2.63-2.763.4210.07914.2714065412041110.9930.09399.8
2.76-2.913.2920.06516.6412906393139210.9940.07899.7
2.91-3.083.3920.05320.3612645374137280.9960.06399.7
3.08-3.33.4820.04324.6312067348434660.9970.05199.5
3.3-3.563.4210.03529.3311118326232500.9980.04299.6
3.56-3.93.2430.03329576297129530.9980.03699.4
3.9-4.363.5170.02737.29550272827150.9990.03299.5
4.36-5.033.4760.02539.628269239123790.9990.0399.5
5.03-6.173.2330.02734.846585204520370.9990.03299.6
6.17-8.723.50.02537.175464157315610.9990.0399.2
8.72-33.1523.2310.0243.4528348948770.9990.02498.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_3500)refinement
PDB_EXTRACT3.25data extraction
MR-Rosettaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BCV_B as per RosettaMR

Resolution: 1.95→33.152 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.88
RfactorNum. reflection% reflectionSelection details
Rfree0.1835 2075 2.76 %0
Rwork0.151 ---
obs0.1519 75188 99.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.2 Å2 / Biso mean: 34.6296 Å2 / Biso min: 14.03 Å2
Refinement stepCycle: final / Resolution: 1.95→33.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6165 0 146 723 7034
Biso mean--60.43 42.93 -
Num. residues----767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076627
X-RAY DIFFRACTIONf_angle_d0.7438989
X-RAY DIFFRACTIONf_dihedral_angle_d13.0364060
X-RAY DIFFRACTIONf_chiral_restr0.056984
X-RAY DIFFRACTIONf_plane_restr0.0041175
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9501-1.99540.2561350.23564479461492
1.9954-2.04530.26051610.21214803496498
2.0453-2.10060.22181200.186648925012100
2.1006-2.16240.21591210.168949515072100
2.1624-2.23220.20681400.168648925032100
2.2322-2.3120.22761550.17464860501599
2.312-2.40450.21681420.162248755017100
2.4045-2.51390.20761370.152249105047100
2.5139-2.64640.19811180.155549605078100
2.6464-2.81210.17591600.155148755035100
2.8121-3.02910.20661210.157249155036100
3.0291-3.33370.19281300.150849385068100
3.3337-3.81550.1571530.139548635016100
3.8155-4.80480.13331350.113149435078100
4.8048-33.15690.17021470.1484957510499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.81910.8109-1.62553.8088-1.54497.1559-0.0116-0.1803-0.12780.2672-0.0324-0.155-0.03050.3906-0.03350.1960.0719-0.03610.2089-0.00250.2663-11.7559-25.222110.6991
26.60913.4438-4.93788.3771-5.8755.613-0.25060.1124-0.3325-0.36770.14710.21710.8887-0.19680.06560.2630.0359-0.0040.1665-0.01630.227-16.0859-31.61334.2885
32.35520.77680.9075.1792-2.15942.1035-0.16280.2054-0.1446-0.1723-0.2512-0.06720.18760.1110.36470.19110.0767-0.00550.1951-0.02570.2586-7.5841-26.3857.0341
41.16920.7366-0.16987.4036-2.15682.2430.0065-0.12270.03550.73830.0677-0.3212-0.00470.1751-0.06020.25720.0573-0.05620.2246-0.02810.2342-7.9352-26.052417.6224
51.2439-0.42751.49892.4841-1.78123.09590.07360.10660.0563-0.0774-0.0127-0.04840.20630.1753-0.08550.15770.03020.01730.1837-0.04370.2181-14.8116-21.40370.0301
63.8051-0.3248-0.34841.36090.92433.59410.0059-0.3347-0.29590.1951-0.030.29890.1899-0.3242-0.01480.14760.01230.01910.17810.02150.2468-26.3189-19.023.7747
72.70490.771.22932.75881.16857.02020.0247-0.14610.110.2551-0.0148-0.0643-0.10110.39530.00090.1894-0.02620.01060.1793-0.0110.2556-9.4659-7.96878.212
86.29531.5579-4.29487.1813-4.31089.67470.1058-0.2860.17370.1812-0.11880.2411-0.6554-0.1792-0.01030.28080.0159-0.00240.2299-0.05780.3456-18.6529-4.32168.1641
95.43982.09211.10845.8799-0.93132.3720.158-0.1815-0.05220.31330.07670.3858-0.083-0.282-0.2410.16180.05920.04810.1672-0.03210.1669-24.2917-17.53062.9409
102.8040.62851.76662.48531.58734.2330.0523-0.16550.01150.1016-0.11360.1294-0.1789-0.07850.0650.2224-0.03880.0330.1609-0.00080.1683.472418.198131.1913
113.30340.22222.32121.18751.46744.80220.0443-0.0268-0.0331-0.0694-0.00520.0289-0.0944-0.0151-0.02830.1822-0.0160.03210.12060.01090.16842.298411.146119.1728
124.5875-2.01671.08033.6204-0.60873.8874-0.0505-0.21880.01830.3212-0.0191-0.0830.1580.07680.09950.2152-0.04290.02060.16580.00320.19022.53032.56722.1092
131.8527-1.6069-1.19775.03572.18151.13050.0255-1.19620.05411.5751-0.0804-0.08250.13560.1878-0.02610.591-0.14560.10340.5968-0.05790.3479-8.7531.334531.5825
145.52830.9654-0.22633.11971.60042.49870.1538-0.1522-0.24180.3501-0.0628-0.01050.1869-0.0217-0.10650.2211-0.00920.01790.11430.04270.13282.91361.458820.9356
154.19220.8853-2.12552.343-1.45066.19440.1695-0.1869-0.00220.2353-0.199-0.0510.1404-0.0440.04070.2663-0.0808-0.02570.14820.02240.199723.041628.305427.1401
163.53310.8417-1.37781.8307-0.79772.68420.3216-0.64120.03860.5525-0.4328-0.2935-0.06170.40390.10520.3612-0.1457-0.08950.37550.09670.286927.846826.399236.7373
173.97210.7999-2.68931.7674-2.30914.32990.1029-0.1468-0.11050.1124-0.1214-0.0562-0.03020.10170.00040.2155-0.0414-0.01520.1357-0.00580.202626.277934.671919.3518
183.5423-1.6284-1.11574.28681.084.0035-0.0707-0.1435-0.06420.3454-0.03460.0082-0.07770.10490.05130.2452-0.0414-0.02730.1690.02750.183925.785943.84118.6344
194.0252-0.7686-0.39184.6668-0.47385.10130.0903-0.4721-0.20890.7045-0.1910.6593-0.2816-0.38740.07460.3319-0.04110.09450.2672-0.04450.379417.867146.1226.3375
204.4176-1.05850.37114.27610.35283.98690.0276-0.3638-0.21410.5433-0.1624-0.8470.09340.76210.07160.2505-0.0346-0.07360.34340.09190.331638.501737.761921.6651
211.4306-1.6571.52484.9853-1.66655.8460.1458-1.3246-0.46971.6122-0.4184-0.2647-0.0657-0.11240.23790.6331-0.2424-0.12280.6160.15790.431637.150944.27731.0934
224.31360.11780.74373.2859-0.8532.43370.1657-0.2274-0.03060.5234-0.15770.0266-0.1647-0.04790.00880.2718-0.0585-0.00450.145-0.00870.132225.264644.221522.0919
232.2359-0.7421-0.59214.7402-1.77783.4909-0.0920.10080.0226-0.0284-0.0541-0.1907-0.27570.31950.0680.1656-0.0550.03070.185-0.02380.214416.433210.2093-11.0902
244.9784-2.34843.75536.8921-4.69264.4581-0.0472-0.04450.17150.32190.24970.2845-0.78390.0041-0.20050.2423-0.04190.05060.1361-0.00530.185112.132616.6735-4.832
251.7027-0.5662-0.20113.4275-1.53678.1748-0.0245-0.12050.01690.0925-0.0244-0.225-0.21140.56490.06360.1779-0.05850.02780.2285-0.01310.233620.596411.2728-7.4248
261.4197-0.42120.55494.19-1.97813.3606-0.02450.0841-0.0578-0.3272-0.0279-0.2534-0.09980.34280.06020.2028-0.04880.05340.236-0.01650.210320.378311.154-17.9586
276.5323-1.8708-0.67283.8782-1.56553.50810.0881-0.0434-0.12290.05280.0020.0062-0.16160.2696-0.08940.144-0.0390.00990.1154-0.03480.150813.59967.2105-5.6951
285.0191-0.62931.76662.0968-0.66135.5116-0.01310.11670.1749-0.00490.01710.1888-0.2244-0.14480.0060.1421-0.01720.03860.1311-0.00860.18414.823.9125-1.3525
292.3346-1.3932-1.75023.21292.13988.8330.05370.1193-0.0577-0.2351-0.0818-0.03590.1820.3085-0.01540.15190.03390.00430.1729-0.00380.22218.7287-7.2915-8.9901
309.2449-1.84174.26672.9534-2.60143.16290.29570.5085-0.7877-0.2984-0.05630.45760.7558-0.0208-0.30470.27850.00810.01080.2086-0.0690.34389.4763-10.8015-8.9855
314.8236-1.3947-1.34945.5606-0.90662.87930.10580.1297-0.0159-0.31710.10560.21440.0538-0.2553-0.23450.1465-0.0453-0.02550.1554-0.05290.12074.28512.0768-3.0141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 27 )A10 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 41 )A28 - 41
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 52 )A42 - 52
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 89 )A53 - 89
5X-RAY DIFFRACTION5chain 'A' and (resid 90 through 119 )A90 - 119
6X-RAY DIFFRACTION6chain 'A' and (resid 120 through 154 )A120 - 154
7X-RAY DIFFRACTION7chain 'A' and (resid 155 through 175 )A155 - 175
8X-RAY DIFFRACTION8chain 'A' and (resid 176 through 185 )A176 - 185
9X-RAY DIFFRACTION9chain 'A' and (resid 186 through 202 )A186 - 202
10X-RAY DIFFRACTION10chain 'B' and (resid 11 through 90 )B11 - 90
11X-RAY DIFFRACTION11chain 'B' and (resid 91 through 119 )B91 - 119
12X-RAY DIFFRACTION12chain 'B' and (resid 120 through 164 )B120 - 164
13X-RAY DIFFRACTION13chain 'B' and (resid 165 through 184 )B165 - 184
14X-RAY DIFFRACTION14chain 'B' and (resid 185 through 201 )B185 - 201
15X-RAY DIFFRACTION15chain 'C' and (resid 11 through 52 )C11 - 52
16X-RAY DIFFRACTION16chain 'C' and (resid 53 through 90 )C53 - 90
17X-RAY DIFFRACTION17chain 'C' and (resid 91 through 119 )C91 - 119
18X-RAY DIFFRACTION18chain 'C' and (resid 120 through 133 )C120 - 133
19X-RAY DIFFRACTION19chain 'C' and (resid 134 through 153 )C134 - 153
20X-RAY DIFFRACTION20chain 'C' and (resid 154 through 164 )C154 - 164
21X-RAY DIFFRACTION21chain 'C' and (resid 165 through 184 )C165 - 184
22X-RAY DIFFRACTION22chain 'C' and (resid 185 through 202 )C185 - 202
23X-RAY DIFFRACTION23chain 'D' and (resid 10 through 27 )D10 - 27
24X-RAY DIFFRACTION24chain 'D' and (resid 28 through 41 )D28 - 41
25X-RAY DIFFRACTION25chain 'D' and (resid 42 through 52 )D42 - 52
26X-RAY DIFFRACTION26chain 'D' and (resid 53 through 89 )D53 - 89
27X-RAY DIFFRACTION27chain 'D' and (resid 90 through 108 )D90 - 108
28X-RAY DIFFRACTION28chain 'D' and (resid 109 through 154 )D109 - 154
29X-RAY DIFFRACTION29chain 'D' and (resid 155 through 175 )D155 - 175
30X-RAY DIFFRACTION30chain 'D' and (resid 176 through 185 )D176 - 185
31X-RAY DIFFRACTION31chain 'D' and (resid 186 through 202 )D186 - 202

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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