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- PDB-3l23: Crystal structure of Sugar phosphate isomerase/epimerase (YP_0013... -

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Basic information

Entry
Database: PDB / ID: 3l23
TitleCrystal structure of Sugar phosphate isomerase/epimerase (YP_001303399.1) from Parabacteroides distasonis ATCC 8503 at 1.70 A resolution
ComponentsSugar phosphate isomerase/epimerase
KeywordsISOMERASE / Sugar phosphate isomerase/epimerase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


isomerase activity / metal ion binding
Similarity search - Function
: / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
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 Sugar phosphate isomerase/epimerase (YP_001303399.1) from Parabacteroides distasonis ATCC 8503 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 17, 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 27, 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

Downloads & links

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Assembly

Deposited unit
A: Sugar phosphate isomerase/epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3697
Polymers35,0341
Non-polymers3356
Water4,864270
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Sugar phosphate isomerase/epimerase
hetero molecules

A: Sugar phosphate isomerase/epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,73814
Polymers70,0692
Non-polymers66912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3180 Å2
ΔGint-6 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.657, 56.634, 78.188
Angle α, β, γ (deg.)90.000, 102.980, 90.000
Int Tables number5
Space group name H-MC121
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Sugar phosphate isomerase/epimerase


Mass: 35034.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_2046 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LDL3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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. THE CLONED CONSTRUCT CONTAINS RESIDUES 33-334 OF THE FULL LENGTH PROTEIN.

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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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 0.2000M MgAcetate, 20.0000% PEG-3350, No Buffer pH 7.7, 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: 0.91837,0.97935
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 8, 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
20.979351
ReflectionResolution: 1.7→28.318 Å / Num. obs: 36149 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 2.81 % / Biso Wilson estimate: 19.269 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 9.45
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.7-1.760.3391.9795306555192.7
1.76-1.830.2512.6100596880197.1
1.83-1.910.193.498156730196.9
1.91-2.020.1414.6110407545197.1
2.02-2.140.0966.495706540197.1
2.14-2.310.0688.6105107144197.1
2.31-2.540.05410.8102576925197.3
2.54-2.90.0413.8100126753196.7
2.9-3.660.0318.8103926951196
3.66-28.3180.02523.6102936801194.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.7→28.318 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 3.52 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.079
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.MAGNESIUM ION FROM CRYSTALLIZATION AND ETHYLENE GLYCOL MOLECULES FROM CRYOPROTECTANT ARE MODELED IN THE STRUCTURE, RESPECTIVELY.
RfactorNum. reflection% reflectionSelection details
Rfree0.167 1806 5 %RANDOM
Rwork0.148 ---
obs0.149 36149 99.07 %-
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: 70.29 Å2 / Biso mean: 34.044 Å2 / Biso min: 16.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.22 Å2
2--1.51 Å20 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 21 270 2476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222350
X-RAY DIFFRACTIONr_bond_other_d0.0020.021587
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.9593173
X-RAY DIFFRACTIONr_angle_other_deg1.0233898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2995302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25125.294102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56215417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.353156
X-RAY DIFFRACTIONr_chiral_restr0.080.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022658
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02458
X-RAY DIFFRACTIONr_nbd_refined0.2110.3467
X-RAY DIFFRACTIONr_nbd_other0.1750.31623
X-RAY DIFFRACTIONr_nbtor_refined0.1830.51153
X-RAY DIFFRACTIONr_nbtor_other0.0880.51117
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.5346
X-RAY DIFFRACTIONr_metal_ion_refined0.0030.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.32
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2180.334
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.525
X-RAY DIFFRACTIONr_mcbond_it1.0311.51596
X-RAY DIFFRACTIONr_mcbond_other0.2551.5594
X-RAY DIFFRACTIONr_mcangle_it1.38522358
X-RAY DIFFRACTIONr_scbond_it2.3753983
X-RAY DIFFRACTIONr_scangle_it3.0624.5814
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 131 -
Rwork0.207 2428 -
all-2559 -
obs--96.13 %
Refinement TLS params.Method: refined / Origin x: 6.0051 Å / Origin y: 4.6327 Å / Origin z: 17.6303 Å
111213212223313233
T-0.1981 Å20.0051 Å2-0.007 Å2--0.1841 Å20.001 Å2---0.1716 Å2
L1.7138 °21.0473 °2-0.1504 °2-1.456 °20.1619 °2--1.5884 °2
S0.0531 Å °-0.1306 Å °0.0868 Å °0.0711 Å °-0.0815 Å °0.0172 Å °-0.0388 Å °0.0724 Å °0.0284 Å °

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