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- PDB-3obe: Crystal structure of a sugar phosphate isomerase/epimerase (BDI_3... -

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Basic information

Entry
Database: PDB / ID: 3obe
TitleCrystal structure of a sugar phosphate isomerase/epimerase (BDI_3400) from Parabacteroides distasonis ATCC 8503 at 1.70 A resolution
ComponentsSugar phosphate isomerase/epimerase
KeywordsISOMERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


: / 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
ETHANOL / PHOSPHATE ION / Sugar phosphate isomerase/epimerase
Similarity search - Component
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a sugar phosphate isomerase/epimerase (BDI_3400) from Parabacteroides distasonis ATCC 8503 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Sugar phosphate isomerase/epimerase
B: Sugar phosphate isomerase/epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,88314
Polymers70,2322
Non-polymers65112
Water10,341574
1
A: Sugar phosphate isomerase/epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4417
Polymers35,1161
Non-polymers3256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sugar phosphate isomerase/epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4417
Polymers35,1161
Non-polymers3256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.745, 48.690, 79.880
Angle α, β, γ (deg.)77.800, 74.670, 68.900
Int Tables number1
Space group name H-MP1
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS THE A PROBABLE OLIGOMERIZATION STATE. HOWEVER, CRYSTAL PACKING DOES NOT INDICATE A STABLE DIMER.

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Components

#1: Protein Sugar phosphate isomerase/epimerase


Mass: 35116.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / Gene: BDI_3400 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LHD8
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT (27-330) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT (27-330) 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.56
Details: 5.0% polyethylene glycol 1000, 32.9% Ethanol, 0.1M phosphate-citrate pH 4.56, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97910
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 4, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.97911
ReflectionResolution: 1.7→27.437 Å / Num. obs: 64918 / % possible obs: 87.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.188 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 10.89
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.761.990.2522.2122091083680.8
1.76-1.830.1862.9127781138784.5
1.83-1.910.1434124721114285
1.91-2.020.095.5140541265886.2
2.02-2.140.0667.6122741110386.4
2.14-2.310.0489.7133911220387.5
2.31-2.540.03812129241184288.3
2.54-2.90.03115.4128541193589.8
2.9-3.660.02321132391245991.2
3.66-27.4370.02125.8132051269893.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SOLVEphasing
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.7→27.437 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 3.191 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.086
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. ETHANOL (EOH) AND PHOSPHATE (PO4) FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1637 3301 5.1 %RANDOM
Rwork0.1398 ---
obs0.141 64915 96.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 76 Å2 / Biso mean: 24.0093 Å2 / Biso min: 9.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å2-0.26 Å2-0.5 Å2
2---0.25 Å20.52 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4589 0 40 574 5203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225016
X-RAY DIFFRACTIONr_bond_other_d0.0010.023487
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.9626796
X-RAY DIFFRACTIONr_angle_other_deg1.22938523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4165641
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23524.959244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13615897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8361523
X-RAY DIFFRACTIONr_chiral_restr0.0970.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215695
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021017
X-RAY DIFFRACTIONr_mcbond_it0.9311.53035
X-RAY DIFFRACTIONr_mcbond_other0.2841.51235
X-RAY DIFFRACTIONr_mcangle_it1.61124901
X-RAY DIFFRACTIONr_scbond_it2.4331981
X-RAY DIFFRACTIONr_scangle_it3.84.51880
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 234 -
Rwork0.201 4482 -
all-4716 -
obs--94.74 %
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)
11.30250.43330.30031.0479-0.14460.968-0.05330.05440.0281-0.08380.04480.0215-0.0043-0.04480.00850.02080.0078-0.0070.0316-0.00840.035161.87436.969.653
21.412-0.4445-0.0411.0041-0.16450.7116-0.0456-0.091-0.02040.1030.0413-0.0215-0.0299-0.00560.00440.025-0.00950.00480.0468-0.00340.027563.57417.37842.173
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 93
2X-RAY DIFFRACTION1A98 - 211
3X-RAY DIFFRACTION1A220 - 330
4X-RAY DIFFRACTION2B39 - 94
5X-RAY DIFFRACTION2B97 - 330

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