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- PDB-3cny: Crystal structure of a putative inositol catabolism protein iole ... -

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Basic information

Entry
Database: PDB / ID: 3cny
TitleCrystal structure of a putative inositol catabolism protein iole (iole, lp_3607) from lactobacillus plantarum wcfs1 at 1.85 A resolution
ComponentsInositol catabolism protein IolE
KeywordsBIOSYNTHETIC PROTEIN / xylose isomerase-like tim barrel / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


myo-inosose-2 dehydratase / myo-inosose-2 dehydratase activity / inositol catabolic process / manganese ion binding
Similarity search - Function
Inosose dehydratase / IolE/MocC family / : / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Inosose dehydratase
Similarity search - Component
Biological speciesLactobacillus plantarum WCFS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative Inositol Catabolism Protein IolE (NP_786806.1) from Lactobacillus plantarum at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inositol catabolism protein IolE
B: Inositol catabolism protein IolE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9639
Polymers68,5312
Non-polymers4317
Water13,493749
1
A: Inositol catabolism protein IolE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3903
Polymers34,2661
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Inositol catabolism protein IolE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5736
Polymers34,2661
Non-polymers3075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.235, 51.553, 246.908
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAPHEPHEAA5 - 446 - 45
21ALAALAPHEPHEBB5 - 446 - 45
32GLYGLYASPASPAA46 - 19747 - 198
42GLYGLYASPASPBB46 - 19747 - 198
53TYRTYRARGARGAA200 - 220201 - 221
63TYRTYRARGARGBB200 - 220201 - 221
74SERSERALAALAAA222 - 289223 - 290
84SERSERALAALABB222 - 289223 - 290

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Components

#1: Protein Inositol catabolism protein IolE


Mass: 34265.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum WCFS1 (bacteria)
Species: Lactobacillus plantarum / Strain: WCFS1 / NCIMB 8826 / Gene: NP_786806.1, iolE, lp_3607 / Plasmid: SpeedE5T / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q88S37
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 749 / 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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: NANODROP, 0.2M (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: 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: 1.8→29.273 Å / Num. obs: 57200 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.373 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.860.742.3354841063695.9
1.86-1.940.5493.3470231261499.9
1.94-2.030.3994.5451741201099.8
2.03-2.130.2676.5417011104599.8
2.13-2.270.2038.3467181231699.8
2.27-2.440.15810.24390911506100
2.44-2.690.11712.8457971200199.9
2.69-3.070.07817440891150699.9
3.07-3.870.04525455311190199.9
3.87-29.2730.03629.6444261180899

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
XDSdata reduction
autoSHARPphasing
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→29.273 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.773 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.127
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. EDO AND ACT FROM THE CRYSTALLIZATION/BUFFER WERE MODELED. 4. THE WATER 10 AND 11 POSITIONS ARE LOCATED IN THE ACTIVE SITES AND ARE LIKELY REPLACED BY METALS IN AN ACTIVE ENZYME.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2891 5.1 %RANDOM
Rwork0.165 ---
obs0.167 57116 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.493 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å20 Å20 Å2
2---0.55 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4747 0 28 749 5524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224989
X-RAY DIFFRACTIONr_bond_other_d0.0030.023375
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9466765
X-RAY DIFFRACTIONr_angle_other_deg0.95238253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7845629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.59624.98251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71815855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.571522
X-RAY DIFFRACTIONr_chiral_restr0.0940.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025638
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02998
X-RAY DIFFRACTIONr_nbd_refined0.2080.21029
X-RAY DIFFRACTIONr_nbd_other0.1930.23707
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22392
X-RAY DIFFRACTIONr_nbtor_other0.0870.22461
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2639
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.237
X-RAY DIFFRACTIONr_mcbond_it1.88833297
X-RAY DIFFRACTIONr_mcbond_other0.69631240
X-RAY DIFFRACTIONr_mcangle_it2.4654874
X-RAY DIFFRACTIONr_scbond_it4.31982176
X-RAY DIFFRACTIONr_scangle_it5.323111875
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1646TIGHT POSITIONAL0.080.1
2049MEDIUM POSITIONAL0.20.25
1646TIGHT THERMAL0.681
2049MEDIUM THERMAL1.343
LS refinement shellResolution: 1.85→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 203 -
Rwork0.234 3825 -
all-4028 -
obs--96.69 %

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