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- PDB-3lmz: Crystal structure of Putative sugar isomerase. (YP_001305105.1) f... -

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Basic information

Entry
Database: PDB / ID: 3lmz
TitleCrystal structure of Putative sugar isomerase. (YP_001305105.1) from Parabacteroides distasonis ATCC 8503 at 1.44 A resolution
ComponentsPutative sugar isomerase
KeywordsISOMERASE / Putative sugar isomerase. / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Xylose isomerase-like TIM barrel domain-containing protein
Similarity search - Component
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.44 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative sugar isomerase. (YP_001305105.1) from Parabacteroides distasonis ATCC 8503 at 1.44 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 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 / 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 / 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: Putative sugar isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9524
Polymers29,5041
Non-polymers4483
Water7,386410
1
A: Putative sugar isomerase
hetero molecules

A: Putative sugar isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9048
Polymers59,0072
Non-polymers8976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4440 Å2
ΔGint1 kcal/mol
Surface area20330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.594, 81.906, 95.485
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-453-

HOH

21A-485-

HOH

DetailsSTATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative sugar isomerase


Mass: 29503.688 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_3797 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LIG9
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 28-283) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 28-283) 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.57
Details: 19.5000% polyethylene glycol 3000, 0.1M citric acid pH 5.57, NANODROP, 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: 0.91162,0.97944,0.97932
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 6, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979441
30.979321
ReflectionResolution: 1.44→28.355 Å / Num. obs: 47272 / % possible obs: 76.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.141 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 10.02
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.44-1.490.491.8186588307179
1.49-1.550.3742.3200908773181.2
1.55-1.620.2923.1201798668180.4
1.62-1.710.2054.3213119049179.6
1.71-1.810.1555.7188957890178.7
1.81-1.950.1028.5205998458177.4
1.95-2.150.06812.4207348316175.8
2.15-2.460.05316.6203197984173.9
2.46-3.10.0421.2203717744171.7
3.1-28.3550.0328.2204707549169.7

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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: 1.44→28.355 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / Occupancy max: 1 / Occupancy min: 0.22 / SU B: 2.072 / SU ML: 0.041 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.068
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. A CITRATE (CIT) MOLECULE IS MODELLED FROM CRYSTALLIZATION CONDITIONS, AND PEG-3000 FRAGMENT FROM CRYSTALLIZATION OR PEG-400 FRAGMENT FROM CRYO CONDITIONS (PEG AND PGE) ARE MODELED. 5. THE NOMINAL RESOLUTION IS 1.55 A WITH 9570 OBSERVED REFLECTIONS BETWEEN 1.55-1.44 A (87.7% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.185 2401 5.1 %RANDOM
Rwork0.149 ---
obs0.151 47252 84.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.95 Å2 / Biso mean: 19.044 Å2 / Biso min: 8.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2--0.96 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.44→28.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 30 410 2443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222191
X-RAY DIFFRACTIONr_bond_other_d0.0020.021508
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.9792971
X-RAY DIFFRACTIONr_angle_other_deg0.97933690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7265272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27123.7596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25715385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4981511
X-RAY DIFFRACTIONr_chiral_restr0.1070.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022448
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02442
X-RAY DIFFRACTIONr_nbd_refined0.2450.2475
X-RAY DIFFRACTIONr_nbd_other0.1930.21574
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21062
X-RAY DIFFRACTIONr_nbtor_other0.0860.21039
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2265
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2620.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.234
X-RAY DIFFRACTIONr_mcbond_it1.76331465
X-RAY DIFFRACTIONr_mcbond_other0.4573529
X-RAY DIFFRACTIONr_mcangle_it2.10452156
X-RAY DIFFRACTIONr_scbond_it4.0698965
X-RAY DIFFRACTIONr_scangle_it5.4911815
LS refinement shellResolution: 1.44→1.478 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 186 -
Rwork0.245 3322 -
all-3508 -
obs--86.23 %
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)
10.25810.17830.35990.5870.16710.51630.0247-0.0473-0.0205-0.0035-0.01080.03740.0412-0.0497-0.0139-0.0304-0.0085-0.0015-0.0056-0.0009-0.00593.558726.960639.5202
20.4398-0.10580.45150.0662-0.06060.67360.04960.0247-0.0430.0032-0.0045-0.02660.08370.0854-0.0451-0.01240.0114-0.0135-0.01190-0.000118.079818.119637.205
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 103
2X-RAY DIFFRACTION2A104 - 283

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