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- PDB-3cgx: Crystal structure of putative nucleotide-diphospho-sugar transfer... -

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Basic information

Entry
Database: PDB / ID: 3cgx
TitleCrystal structure of putative nucleotide-diphospho-sugar transferase (YP_389115.1) from Desulfovibrio desulfuricans G20 at 1.90 A resolution
ComponentsPutative nucleotide-diphospho-sugar transferase
KeywordsTRANSFERASE / YP_389115.1 / Putative Nucleotide-diphospho-sugar Transferase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyTransferase 1, rSAM/selenodomain-associated / Uncharacterized protein conserved in bacteria (DUF2064) / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta / IMIDAZOLE / Glycosyltransferase
Function and homology information
Biological speciesDesulfovibrio desulfuricans subsp. desulfuricans str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative Nucleotide-diphospho-sugar Transferase (YP_389115.1) from Desulfovibrio desulfuricans G20 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / 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 1.5Nov 6, 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: Putative nucleotide-diphospho-sugar transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1872
Polymers28,1181
Non-polymers691
Water3,585199
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.520, 66.940, 71.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative nucleotide-diphospho-sugar transferase


Mass: 28117.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio desulfuricans subsp. desulfuricans str. (bacteria)
Species: Desulfovibrio desulfuricans / Strain: G20 / Gene: YP_389115.1, Dde_2624 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q30Y26
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: NANODROP, 20.0% Glycerol, 0.04M KH2PO4, 16.0% PEG 8000, No Buffer, 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: 0.97908 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 21, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 1.9→28.8 Å / Num. obs: 22017 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.57 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 10.72
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.9-1.970.4551.9578894164197.6
1.97-2.050.3122.880244205199.8
2.05-2.140.2223.975473955199.7
2.14-2.250.165.377184032199.8
2.25-2.390.1176.879454148199.8
2.39-2.580.0918.482224270199.6
2.58-2.840.06311.578254063199.1
2.84-3.250.04116.479004092199
3.25-4.080.02523.477914032198.5
4.08-28.80.02327.777413996195

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→28.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.874 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.129
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS 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 RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. IMIDAZOLE FROM PROTEIN EXPRESSION IS MODELED IN THIS STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1128 5.1 %RANDOM
Rwork0.171 ---
obs0.173 21971 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.842 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2--0.32 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 5 199 2013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221920
X-RAY DIFFRACTIONr_bond_other_d0.0010.021271
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.9642618
X-RAY DIFFRACTIONr_angle_other_deg1.06733098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7565244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58224.72591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27915306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.673158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212213
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02401
X-RAY DIFFRACTIONr_mcbond_it1.94831191
X-RAY DIFFRACTIONr_mcbond_other0.5563480
X-RAY DIFFRACTIONr_mcangle_it3.21951910
X-RAY DIFFRACTIONr_scbond_it5.1528729
X-RAY DIFFRACTIONr_scangle_it7.41611708
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 74 -
Rwork0.22 1514 -
all-1588 -
obs--98.09 %
Refinement TLS params.Method: refined / Origin x: 25.686 Å / Origin y: 27.918 Å / Origin z: 0.699 Å
111213212223313233
T-0.0942 Å2-0.0113 Å2-0.0133 Å2--0.0472 Å2-0.0077 Å2---0.074 Å2
L1.2019 °2-0.3667 °2-0.4097 °2-1.268 °20.346 °2--1.1011 °2
S0.0076 Å °-0.0519 Å °0.0517 Å °0.0796 Å °-0.0109 Å °0.0153 Å °-0.0712 Å °0.0475 Å °0.0033 Å °

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