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- PDB-6ndr: Crystal structure of dTDP-6-deoxy-D-glucose-3,5-epimerase RmlC fr... -

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Basic information

Entry
Database: PDB / ID: 6ndr
TitleCrystal structure of dTDP-6-deoxy-D-glucose-3,5-epimerase RmlC from Legionella pneumophila Philadelphia 1 in complex with dTDP-4-KETO-L-RHAMNOSE
ComponentsdTDP-4-dehydrorhamnose 3,5-epimerase
KeywordsSUGAR BINDING PROTEIN / SSGCID / dTDP-4-dehydrorhamnose 3 / 5-epimerase / dTDP-6-deoxy-D-glucose-3 / RmlC / lpg0756 / Legionella pneumophila / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process
Similarity search - Function
dTDP-4-dehydrorhamnose 3,5-epimerase-related / dTDP-4-dehydrorhamnose 3,5-epimerase / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
DTDP-4-KETO-L-RHAMNOSE / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of dTDP-6-deoxy-D-glucose-3,5-epimerase RmlC from Legionella pneumophila Philadelphia 1 in complex with dTDP-4-KETO-L-RHAMNOSE
Authors: Abendroth, J. / Schulze, M.-S. / Mayclin, S.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionDec 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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: dTDP-4-dehydrorhamnose 3,5-epimerase
B: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,76215
Polymers44,8852
Non-polymers1,87713
Water9,476526
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-43 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.380, 46.160, 102.030
Angle α, β, γ (deg.)90.000, 112.290, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein dTDP-4-dehydrorhamnose 3,5-epimerase


Mass: 22442.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Gene: lpg0756
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: Q5ZXH5
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TDO / DTDP-4-KETO-L-RHAMNOSE


Mass: 546.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H24N2O15P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Microlytic MCSG1 screen, condition E4: 200mM Lithium sulfate, 25% PEG 3350, 100mM Tris base / HCl pH 8.5: LepnA.18372.a.B1.PW38444 at 17.2mg/ml. Cryo: 20% EG: tray: 300303e4g8: puck uhg9-6.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 26, 2017 / Details: RIGAKU VARIMAX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→47.202 Å / Num. obs: 57363 / % possible obs: 97 % / Redundancy: 4.036 % / Biso Wilson estimate: 26.104 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03 / Rrim(I) all: 0.033 / Χ2: 1.007 / Net I/σ(I): 24.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.642.8350.3593.0238530.8960.44288.9
1.64-1.692.9060.2853.8238370.9190.34991.1
1.69-1.742.9860.2184.9938220.9510.26692.6
1.74-1.793.0590.176.1237850.9730.20694.5
1.79-1.853.1480.1387.6837560.9820.16796.4
1.85-1.913.2330.10310.0336550.9920.12397.8
1.91-1.983.320.08312.5135680.9930.09999.1
1.98-2.073.4080.06316.3234950.9960.07499.7
2.07-2.163.5170.05220.9433680.9970.06199.7
2.16-2.263.6690.04524.5731990.9970.05399.3
2.26-2.393.90.0428.230090.9980.04798.9
2.39-2.534.1650.03832.0128590.9990.04399.3
2.53-2.74.520.03336.3727370.9990.03799.5
2.7-2.924.8910.03140.8524950.9990.034100
2.92-3.25.6440.02847.8523610.9990.03199.7
3.2-3.586.9450.02562.121120.9990.02799.8
3.58-4.137.3070.02268.87187910.02499.7
4.13-5.067.2970.02172.21160310.02399.8
5.06-7.167.1850.02369.04125510.02599.7
7.16-47.2026.750.02469.5471510.02699.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
PDB_EXTRACT3.24data extraction
XSCALEdata scaling
MoRDaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ixi as per MorDa

2ixi


Resolution: 1.6→47.202 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.17
RfactorNum. reflection% reflectionSelection details
Rfree0.1763 1949 3.4 %0
Rwork0.1505 ---
obs0.1514 57344 97.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.86 Å2 / Biso mean: 24.2081 Å2 / Biso min: 10.03 Å2
Refinement stepCycle: final / Resolution: 1.6→47.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3008 0 117 539 3664
Biso mean--34.85 35.76 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093343
X-RAY DIFFRACTIONf_angle_d1.0194571
X-RAY DIFFRACTIONf_dihedral_angle_d14.8212003
X-RAY DIFFRACTIONf_chiral_restr0.073490
X-RAY DIFFRACTIONf_plane_restr0.006605
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.640.22551090.20243591370089
1.64-1.68440.24141520.18883659381191
1.6844-1.73390.21941400.17913728386893
1.7339-1.78990.23961320.1843837396995
1.7899-1.85390.21721300.17993943407396
1.8539-1.92810.19281410.16533976411798
1.9281-2.01590.19261600.15540194179100
2.0159-2.12210.18471410.155340264167100
2.1221-2.25510.18951250.1540894214100
2.2551-2.42920.18391600.14944023418399
2.4292-2.67360.16291210.15594077419899
2.6736-3.06050.18561430.156740964239100
3.0605-3.85560.16051380.130341204258100
3.8556-47.22280.14351570.136542114368100
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)
15.956-0.4514-0.5222.7180.78294.02680.1302-0.01310.3230.17770.12780.0163-0.6182-0.1035-0.25660.17280.0310.02840.0847-0.03450.165917.2947-2.346944.9281
22.52930.07191.06980.9672-0.17573.42340.06480.34160.1333-0.2006-0.03220.0659-0.6906-0.07970.0020.28110.04790.00240.1190.01170.185718.10751.369327.2532
31.29760.4015-0.21140.8294-0.04342.0868-0.0203-0.0146-0.0234-0.0362-0.04010.00240.01390.04180.05360.07810.02780.00560.1018-0.00770.131622.3527-14.939435.7426
41.1214-0.00160.17670.7331-0.41822.815-0.00590.02220.0055-0.0252-0.0224-0.0067-0.0457-0.1580.01970.07470.0091-0.00120.1003-0.00490.124913.5788-12.345240.612
50.58830.1378-0.90590.5484-0.59161.5593-0.0538-0.0006-0.2034-0.0978-0.01580.02210.2662-0.06010.06040.1486-0.0094-0.00940.1127-0.02030.182620.8468-21.530134.9641
61.5939-0.2515-0.13524.47830.75323.35220.040.081-0.244-0.1485-0.10020.1610.2966-0.41610.02990.1115-0.07120.01310.1738-0.03320.20614.8269-23.2341.7625
76.60154.3210.79487.53180.94230.99950.1003-0.4458-0.47550.1169-0.1326-0.39120.1514-0.0264-0.01790.11540.00210.00920.13290.0320.133620.4315-25.379552.0251
82.26980.2593-1.40441.4724-0.47253.2623-0.17520.0856-0.2056-0.12170.0250.07640.4249-0.13260.29770.20250.0120.00870.1144-0.02750.168525.1054-20.532817.1328
92.67340.9359-0.08353.1021.51765.84580.00120.1449-0.2939-0.08340.0166-0.27060.25970.6138-0.04570.16940.04370.00460.25540.00070.177335.4409-15.773223.6232
101.09820.1697-0.32270.8-0.21862.39870.01150.07260.0416-0.0376-0.029-0.0529-0.19240.02140.01770.16330.00730.00530.1290.00920.122326.1114-5.624212.0741
110.16250.3145-0.58850.6777-0.80422.24340.06790.12320.17970.0549-0.0501-0.0098-0.5410.06440.02110.2657-0.00140.01940.15150.01550.190827.5460.678418.794
122.68890.369-1.38734.7790.97913.76630.15680.26240.2345-0.1555-0.14340.1252-0.3984-0.2361-0.05280.28770.07870.00320.17240.04730.133921.6652.40542.6199
139.2256-2.12471.37225.3265-1.34015.99010.07280.29660.1540.1767-0.2263-0.2532-0.36560.65140.17730.2523-0.07640.01860.24330.05070.129938.54454.96886.053
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 11 )A0 - 11
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 31 )A12 - 31
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 70 )A32 - 70
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 125 )A71 - 125
5X-RAY DIFFRACTION5chain 'A' and (resid 126 through 145 )A126 - 145
6X-RAY DIFFRACTION6chain 'A' and (resid 146 through 169 )A146 - 169
7X-RAY DIFFRACTION7chain 'A' and (resid 170 through 187 )A170 - 187
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 31 )B0 - 31
9X-RAY DIFFRACTION9chain 'B' and (resid 32 through 46 )B32 - 46
10X-RAY DIFFRACTION10chain 'B' and (resid 47 through 125 )B47 - 125
11X-RAY DIFFRACTION11chain 'B' and (resid 126 through 145 )B126 - 145
12X-RAY DIFFRACTION12chain 'B' and (resid 146 through 169 )B146 - 169
13X-RAY DIFFRACTION13chain 'B' and (resid 170 through 187 )B170 - 187

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