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- PDB-6din: High resolutionstructure of apo dTDP-4-dehydrorhamnose 3,5-epimerase -

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Basic information

Entry
Database: PDB / ID: 6din
TitleHigh resolutionstructure of apo dTDP-4-dehydrorhamnose 3,5-epimerase
ComponentsdTDP-4-dehydrorhamnose 3,5-epimerase
KeywordsISOMERASE / epimerase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / NIAID / CSGID
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-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsChang, C. / Jedrzejczak, R. / Chhor, G. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: High resolutionstructure of apo dTDP-4-dehydrorhamnose 3,5-epimerase
Authors: Chang, C. / Jedrzejczak, R. / Chhor, G. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5445
Polymers21,1591
Non-polymers3844
Water3,567198
1
A: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules

A: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,08710
Polymers42,3192
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4010 Å2
ΔGint-102 kcal/mol
Surface area17400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.854, 58.854, 160.908
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein dTDP-4-dehydrorhamnose 3,5-epimerase / Thymidine diphospho-4-keto-rhamnose 3 / 5-epimerase


Mass: 21159.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: rmlC, rfbC, CAZ03_15755, HV91_29470, PAERUG_E15_London_28_01_14_02405, RW109_RW109_06764
Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D6IV69, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.31 Å3/Da / Density % sol: 62.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Sodium Chloride, bis-Tris, Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2011
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 27242 / % possible obs: 99.9 % / Redundancy: 11.2 % / Biso Wilson estimate: 28.76 Å2 / Rmerge(I) obs: 0.084 / Χ2: 2.004 / Net I/σ(I): 9.3 / Num. measured all: 303807
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsΧ2Diffraction-ID% possible allRmerge(I) obs
1.8-1.829.66651.1181100
1.82-1.8310.26681.09311000.946
1.83-1.8510.56651.16811000.979
1.85-1.8610.96581.0971100
1.86-1.8811.26671.15111000.873
1.88-1.911.36771.18811000.904
1.9-1.9211.56411.17811000.658
1.92-1.9411.66811.14811000.621
1.94-1.9611.66721.13211000.587
1.96-1.9811.66631.15711000.584
1.98-211.66491.19311000.475
2-2.0311.76861.16911000.371
2.03-2.0511.66471.16911000.384
2.05-2.0811.66831.15711000.33
2.08-2.1111.66711.23311000.307
2.11-2.1311.66591.28911000.269
2.13-2.1611.66801.17711000.247
2.16-2.211.66751.26911000.217
2.2-2.2311.66531.311000.222
2.23-2.2711.66971.49111000.213
2.27-2.3111.66431.31111000.174
2.31-2.3511.66931.35911000.175
2.35-2.3911.56641.35511000.163
2.39-2.4411.56911.47611000.154
2.44-2.511.56491.48111000.136
2.5-2.5511.66961.53411000.123
2.55-2.6211.46791.75711000.114
2.62-2.6911.46881.78611000.106
2.69-2.7711.46712.06411000.1
2.77-2.8611.36892.27911000.095
2.86-2.9611.36832.48911000.085
2.96-3.0811.26922.88811000.083
3.08-3.22116843.34311000.076
3.22-3.39116883.522199.90.066
3.39-3.610.86993.48711000.061
3.6-3.8810.57043.6311000.055
3.88-4.2710.57113.90211000.05
4.27-4.8810.47273.97511000.045
4.88-6.1510.47276.08611000.058
6.15-508.88077.203197.60.061

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→41.616 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.37
RfactorNum. reflection% reflection
Rfree0.2059 1351 5.02 %
Rwork0.1759 --
obs0.1774 26818 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.74 Å2 / Biso mean: 42.9425 Å2 / Biso min: 23.99 Å2
Refinement stepCycle: final / Resolution: 1.8→41.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 20 198 1708
Biso mean--89.21 50.39 -
Num. residues----184
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7995-1.83420.33161330.33492622275598
1.8342-1.87160.34151190.30262584270398
1.8716-1.91230.35421340.29012612274697
1.9123-1.95680.27391370.23592603274098
1.9568-2.00570.26161480.22222567271599
2.0057-2.05990.25021390.20812617275699
2.0599-2.12050.22721440.19372625276999
2.1205-2.1890.21291620.18552593275598
2.189-2.26720.23881490.19082591274099
2.2672-2.3580.22421400.18762592273298
2.358-2.46530.24791430.2052582272598
2.4653-2.59530.22821500.19162591274198
2.5953-2.75780.27061440.19042566271098
2.7578-2.97070.23751130.19372683279699
2.9707-3.26950.23291510.17152606275799
3.2695-3.74240.15851240.14726402764100
3.7424-4.7140.13711180.125626512769100
4.714-41.62720.16431350.16932647278299
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)
10.4232-0.49920.20040.4526-0.10870.8181-0.0168-0.50420.11090.08790.1249-0.044-0.3355-0.65320.0060.3011-0.005-0.01570.4646-0.02490.31897.265623.91682.9719
20.7556-0.19630.42470.3625-0.08711.58140.06110.02520.0322-0.2027-0.1048-0.0283-0.0137-0.1644-00.3253-0.0462-0.0080.25450.00780.299512.901123.027867.7511
30.6765-0.6710.20750.59920.15170.6061-0.17660.59880.1434-0.48390.20680.0398-0.3406-0.0710.00060.507-0.09340.02330.32610.05950.325213.486528.483955.7865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 46 )A-2 - 46
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 145 )A47 - 145
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 181 )A146 - 181

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