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- PDB-3ejk: Crystal structure of dTDP Sugar Isomerase (YP_390184.1) from DESU... -

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Basic information

Entry
Database: PDB / ID: 3ejk
TitleCrystal structure of dTDP Sugar Isomerase (YP_390184.1) from DESULFOVIBRIO DESULFURICANS G20 at 1.95 A resolution
ComponentsdTDP Sugar Isomerase
KeywordsISOMERASE / YP_390184.1 / dTDP Sugar Isomerase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose 3,5-epimerase activity
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
CITRIC ACID / Unknown ligand / Polysaccharide biosynthesis domain-containing protein
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans subsp. desulfuricans str. G20 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of dTDP Sugar Isomerase (YP_390184.1) from DESULFOVIBRIO DESULFURICANS G20 at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dTDP Sugar Isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0827
Polymers19,3191
Non-polymers7636
Water2,306128
1
A: dTDP Sugar Isomerase
hetero molecules

A: dTDP Sugar Isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,16414
Polymers38,6392
Non-polymers1,52512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area6460 Å2
ΔGint-2 kcal/mol
Surface area13620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.790, 86.510, 51.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsAUTHORS STATE THAT CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein dTDP Sugar Isomerase / Polysaccharide biosynthesis domain protein


Mass: 19319.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio desulfuricans subsp. desulfuricans str. G20 (bacteria)
Gene: YP_390184.1, Dde_3696 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q30V07

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Non-polymers , 5 types, 134 molecules

#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 30.0000% PEG-6000, 0.1M Citrate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97911,0.97932
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 10, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979111
30.979321
ReflectionResolution: 1.95→29.722 Å / Num. obs: 13593 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.509 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 7.09
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.95-2.020.4971.747842516196.9
2.02-2.10.3852.148052510198.7
2.1-2.20.32.851092651198.7
2.2-2.310.2493.346002389198.3
2.31-2.460.1944.150932647199.1
2.46-2.650.1694.848402498198.8
2.65-2.910.1296.248202490198.5
2.91-3.330.07210.249102531198.9
3.33-4.190.04516.149162527198.3
4.19-29.7220.03319.449982563198.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.95→29.722 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.699 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.143
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. CIT, PG4 AND GOL MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTIONS ARE MODELED. 5. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED COVALENTLY ATTACHED TO SG ATOM OF RESIDUE CYSTEINE 83. THIS RESEMBLES CYSTEINE RESIDUE MODIFIED TO THIO METHYLATED CYSTEINE (SCH).
RfactorNum. reflection% reflectionSelection details
Rfree0.217 673 5 %RANDOM
Rwork0.169 ---
obs0.171 13584 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 69.02 Å2 / Biso mean: 27.245 Å2 / Biso min: 14.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2---1.26 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 0 47 128 1386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221320
X-RAY DIFFRACTIONr_bond_other_d0.0020.02910
X-RAY DIFFRACTIONr_angle_refined_deg1.7212.0011804
X-RAY DIFFRACTIONr_angle_other_deg1.41332216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.845166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08522.85756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.36615195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4991511
X-RAY DIFFRACTIONr_chiral_restr0.0880.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211464
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02264
X-RAY DIFFRACTIONr_mcbond_it0.9672801
X-RAY DIFFRACTIONr_mcbond_other0.1772316
X-RAY DIFFRACTIONr_mcangle_it1.84241300
X-RAY DIFFRACTIONr_scbond_it3.3746519
X-RAY DIFFRACTIONr_scangle_it5.0258499
LS refinement shellResolution: 1.951→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 39 -
Rwork0.226 956 -
all-995 -
obs--99 %
Refinement TLS params.Method: refined / Origin x: 8.494 Å / Origin y: 14.632 Å / Origin z: 2.649 Å
111213212223313233
T-0.1268 Å2-0.004 Å2-0.0097 Å2-0.0027 Å2-0.0007 Å2---0.0966 Å2
L0.9209 °20.113 °2-0.4399 °2-0.6192 °2-0.1001 °2--0.739 °2
S-0.0022 Å °0.0673 Å °0.0147 Å °-0.0548 Å °-0.014 Å °-0.0225 Å °-0.0614 Å °-0.0338 Å °0.0162 Å °

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