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- PDB-3p6l: Crystal structure of a Sugar phosphate isomerase/epimerase (BDI_1... -

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Basic information

Entry
Database: PDB / ID: 3p6l
TitleCrystal structure of a Sugar phosphate isomerase/epimerase (BDI_1903) from Parabacteroides distasonis ATCC 8503 at 1.85 A resolution
ComponentsSugar phosphate isomerase/epimerase
KeywordsISOMERASE / TIM BARREL / 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
CITRIC ACID / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Xylose isomerase-like TIM barrel domain-containing protein
Similarity search - Component
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Sugar phosphate isomerase/epimerase (BDI_1903) from Parabacteroides distasonis ATCC 8503 at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 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 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6815
Polymers30,1821
Non-polymers4994
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
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)61,36210
Polymers60,3642
Non-polymers9998
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2870 Å2
ΔGint-11 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.382, 73.014, 47.536
Angle α, β, γ (deg.)90.000, 103.730, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-300-

PO4

DetailsCRYSTAL PACKING ANALYSIS SUGGEST THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Sugar phosphate isomerase/epimerase


Mass: 30181.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / Gene: BDI_1903 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LD74
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT (RESIDUES 24-284) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 24-284) 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.33
Details: 45.5% polyethylene glycol 600, 0.1M phosphate-citrate pH 4.33, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537,0.9796,0.9794
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 16, 2010
RadiationMonochromator: DOUBLE CRYSTAL SI (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97961
30.97941
ReflectionResolution: 1.85→28.638 Å / Num. all: 23324 / Num. obs: 23324 / % possible obs: 99.6 % / Redundancy: 3 % / Biso Wilson estimate: 22.447 Å2 / Rsym value: 0.09 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.930.8180.8533117560.818100
1.9-1.952.90.6120.9485816470.61299.7
1.95-2.0130.5041.4498216350.504100
2.01-2.0730.3821.2490916110.38299.9
2.07-2.1430.2981.7458115110.29899.9
2.14-2.213.10.2153.3455614850.215100
2.21-2.292.90.2351.7431714700.235100
2.29-2.393.10.164.3422213730.16100
2.39-2.493.10.1275.7408513290.127100
2.49-2.623.10.1116.4386512650.111100
2.62-2.7630.0996.9366712110.099100
2.76-2.933.10.0769.1347611330.07699.8
2.93-3.1330.06510.2321810580.06599.3
3.13-3.3830.05212.130309940.05299.1
3.38-3.730.0512.827319130.0598.2
3.7-4.142.90.04513.524308260.04598.8
4.14-4.782.80.04214.820487330.04298.8
4.78-5.853.20.04313.619776250.04399.3
5.85-8.273.20.04215.615294840.04298.9
8.27-28.6383.10.04213.98232650.04295.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→28.638 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 8.046 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.148
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.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.PEG FRAGMENTS (PEG), PHOSPHATE (PO4) AND CITRATE (CIT) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 1197 5.2 %RANDOM
Rwork0.1862 ---
obs0.1889 23228 99.17 %-
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: 63.81 Å2 / Biso mean: 27.5871 Å2 / Biso min: 9.38 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å2-2.4 Å2
2---0.95 Å20 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 1.85→28.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2112 0 32 179 2323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222260
X-RAY DIFFRACTIONr_bond_other_d0.0010.021584
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.9623053
X-RAY DIFFRACTIONr_angle_other_deg0.92633900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9175281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34725.714105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89815430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.707155
X-RAY DIFFRACTIONr_chiral_restr0.10.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022488
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02429
X-RAY DIFFRACTIONr_mcbond_it1.37321333
X-RAY DIFFRACTIONr_mcbond_other0.3022548
X-RAY DIFFRACTIONr_mcangle_it2.33942153
X-RAY DIFFRACTIONr_scbond_it4.0886927
X-RAY DIFFRACTIONr_scangle_it5.7678890
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 93 -
Rwork0.318 1637 -
all-1730 -
obs--98.86 %
Refinement TLS params.Method: refined / Origin x: 18.1669 Å / Origin y: 5.5991 Å / Origin z: 10.9021 Å
111213212223313233
T0.0214 Å20.0045 Å20.0117 Å2-0.0396 Å2-0.0096 Å2--0.0288 Å2
L0.955 °20.1511 °20.0836 °2-1.312 °2-0.1587 °2--1.7891 °2
S0.0064 Å °0.0893 Å °-0.1375 Å °0.0197 Å °0.0013 Å °-0.0436 Å °0.0561 Å °-0.0531 Å °-0.0077 Å °

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