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- PDB-3g68: CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHOSUGAR ISOMERASE (CD3275) F... -

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Basic information

Entry
Database: PDB / ID: 3g68
TitleCRYSTAL STRUCTURE OF A PUTATIVE PHOSPHOSUGAR ISOMERASE (CD3275) FROM CLOSTRIDIUM DIFFICILE 630 AT 1.80 A RESOLUTION
ComponentsPutative phosphosugar isomerase
KeywordsISOMERASE / PUTATIVE PHOSPHOSUGAR ISOMERASE / SIS DOMAIN / DOUBLE-SIS DOMAIN PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


carbohydrate derivative metabolic process / carbohydrate derivative binding / isomerase activity
Similarity search - Function
GlmS/FrlB, SIS domain 2 / GlmS/AgaS, SIS domain 1 / SIS domain / SIS domain / SIS domain profile. / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Putative phosphosugar isomerase
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of double-SIS domain protein (YP_001089791.1) from Clostridium difficile 630 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative phosphosugar isomerase
B: Putative phosphosugar isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,48810
Polymers80,7312
Non-polymers7578
Water11,133618
1
A: Putative phosphosugar isomerase
B: Putative phosphosugar isomerase
hetero molecules

A: Putative phosphosugar isomerase
B: Putative phosphosugar isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,97520
Polymers161,4624
Non-polymers1,51316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4830 Å2
ΔGint-26.2 kcal/mol
Surface area24620 Å2
MethodPISA
2
A: Putative phosphosugar isomerase
B: Putative phosphosugar isomerase
hetero molecules

A: Putative phosphosugar isomerase
B: Putative phosphosugar isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,97520
Polymers161,4624
Non-polymers1,51316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4950 Å2
ΔGint-26.2 kcal/mol
Surface area24620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.525, 55.914, 103.031
Angle α, β, γ (deg.)90.000, 114.220, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-678-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative phosphosugar isomerase


Mass: 40365.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD3275, YP_001089791.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q180C0
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: NANODROP, 0.20M (NH4)2H Citrate, 20.0% PEG 3350, No Buffer pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97967, 0.94645
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 12, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979671
20.946451
ReflectionResolution: 1.8→28.989 Å / Num. obs: 55259 / % possible obs: 88.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 13.458 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 4.412
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.851.60.2473314519400.24743.3
1.85-1.91.70.1953.8372421870.19549.5
1.9-1.951.80.1714.1458024960.17158.4
1.95-2.012.20.2183826137700.21888.9
2.01-2.083.30.2632.61332740960.26399.7
2.08-2.153.40.2153.21341939730.21599.9
2.15-2.233.40.1823.81311138490.182100
2.23-2.323.50.1624.21274236880.16299.9
2.32-2.433.40.154.51216535470.15100
2.43-2.553.40.1383.31151333940.13899.9
2.55-2.683.40.1285.31091332150.128100
2.68-2.853.40.1145.81056430860.114100
2.85-3.043.60.0986.81018728630.09899.9
3.04-3.293.70.0837.5981126730.083100
3.29-3.63.70.0826.9924024810.082100
3.6-4.023.70.0846.9844022620.084100
4.02-4.653.70.078.8744019890.07100
4.65-5.693.70.0669624816850.066100
5.69-8.053.70.0728.5488113320.072100
8.05-28.9893.50.072325697330.07297.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→28.989 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.102 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.128
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. CITRATE AND ETHYLENE GLYCOL MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. THE CITRATE MOLECULE SITS IN THE ACTIVE SITE. 5. REGIONS COVERING RESIDUES B70-83 AND B94-110 HAVE POOR ELECTRON DENSITY. 6. THE TLS DEFINITION WAS GENERATED USING THE TLSMD SERVER.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2802 5.1 %RANDOM
Rwork0.159 ---
obs0.161 55259 88.06 %-
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: 69.57 Å2 / Biso mean: 17.311 Å2 / Biso min: 3.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å2-1.01 Å2
2---1.14 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5427 0 50 618 6095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225689
X-RAY DIFFRACTIONr_bond_other_d0.0020.023813
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9757716
X-RAY DIFFRACTIONr_angle_other_deg1.15739396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8455733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16225.44250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.557151039
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.321524
X-RAY DIFFRACTIONr_chiral_restr0.0990.2889
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026320
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021068
X-RAY DIFFRACTIONr_nbd_refined0.2120.21159
X-RAY DIFFRACTIONr_nbd_other0.1660.24042
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22818
X-RAY DIFFRACTIONr_nbtor_other0.0810.22721
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2490
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0350.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.251
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.2101
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.244
X-RAY DIFFRACTIONr_mcbond_it1.33523660
X-RAY DIFFRACTIONr_mcbond_other0.26921440
X-RAY DIFFRACTIONr_mcangle_it2.08645737
X-RAY DIFFRACTIONr_scbond_it3.73562324
X-RAY DIFFRACTIONr_scangle_it4.98981962
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 106 -
Rwork0.194 1762 -
all-1868 -
obs--40.73 %
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)
10.25480.08310.23450.16670.12820.2350.02840.0183-0.0636-0.03390.0427-0.00070.00090.0214-0.0711-0.0277-0.00420.01210.0102-0.00330.017631.77946.584837.0966
20.8205-0.31670.64861.19460.20970.7101-0.02070.244-0.13-0.02310.1114-0.015-0.02270.1168-0.0907-0.0392-0.00070.03030.0444-0.0691-0.001740.455342.821529.2221
30.27210.05190.09490.48250.09050.04420.0001-0.02-0.0169-0.00730.00580.0385-0.01160.0031-0.0059-0.0183-0.00110.02950.00580.0097-0.007328.921659.210146.2437
42.70260.07170.71730.76560.27360.27520.0507-0.10090.0220.1865-0.02880.14810.028-0.0053-0.0219-0.0074-0.00080.05820.014-0.0081-0.023725.127968.313956.3638
50.09140.11650.16590.23770.19350.3048-0.0039-0.0024-0.0114-0.1051-0.00070.1453-0.03930.0970.0046-0.0001-0.00670.0250.01630.009-0.023631.803965.468337.6806
60.1483-0.29950.38250.6075-0.78651.05910.1792-0.0996-0.0596-0.12630.19950.18850.2574-0.1579-0.37860.0718-0.0534-0.0985-0.01070.06890.02273.570254.263816.847
70.3477-0.5054-0.59090.7370.78063.68060.3143-0.1111-0.02390.02850.2836-0.08690.7255-1.0416-0.59790.0717-0.2859-0.24740.1610.30550.0442-9.99649.21719.3374
80.1654-0.23580.44690.4734-0.77381.34360.1381-0.0203-0.0133-0.12030.11190.04830.1219-0.0632-0.24990.0151-0.0079-0.0309-0.0120.02340.00117.481361.025617.1325
90.476-0.31030.39920.467-0.42831.15620.07610.102-0.0421-0.0223-0.0403-0.01070.03750.146-0.0358-0.0230.00550.01050.0206-0.0152-0.018813.888874.10212.0963
100.1603-0.00770.19210.01220.04870.51590.0854-0.0227-0.05940.09360.0118-0.02770.0509-0.1117-0.09720.0255-0.00630.02650.02620.0273-0.0201-0.302471.5414.8424
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 75
2X-RAY DIFFRACTION2A76 - 133
3X-RAY DIFFRACTION3A134 - 274
4X-RAY DIFFRACTION4A275 - 304
5X-RAY DIFFRACTION5A305 - 344
6X-RAY DIFFRACTION6B0 - 69
7X-RAY DIFFRACTION7B70 - 107
8X-RAY DIFFRACTION8B108 - 227
9X-RAY DIFFRACTION9B228 - 304
10X-RAY DIFFRACTION10B305 - 350

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