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- PDB-3kws: Crystal structure of Putative sugar isomerase (YP_001305149.1) fr... -

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Basic information

Entry
Database: PDB / ID: 3kws
TitleCrystal structure of Putative sugar isomerase (YP_001305149.1) from Parabacteroides distasonis ATCC 8503 at 1.68 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
DI(HYDROXYETHYL)ETHER / AP_endonuc_2 domain-containing protein
Similarity search - Component
Biological speciesParabacteroides distasonis ATCC 8503 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.68 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative sugar isomerase (YP_001305149.1) from Parabacteroides distasonis ATCC 8503 at 1.68 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: 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: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_distant_solvent_atoms / pdbx_struct_conn_angle ...pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / software / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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 / _software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 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.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.ptnr1_auth_asym_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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative sugar isomerase
B: Putative sugar isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7567
Polymers63,3892
Non-polymers3675
Water14,736818
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-6 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.573, 107.200, 113.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A48 - 312
2115B48 - 312
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Putative sugar isomerase


Mass: 31694.359 Da / Num. of mol.: 2 / Fragment: residues 27-312
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis ATCC 8503 (bacteria)
Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_3843 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LIL3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 818 / Source method: isolated from a natural source / Formula: H2O
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 27-312 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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2000M MgCl2, 20.0000% PEG-8000, 0.1M TRIS pH 8.5, 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: 0.91837,0.97910,0.97858
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 11, 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
30.978581
ReflectionResolution: 1.68→29.374 Å / Num. obs: 71903 / % possible obs: 99.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 11.88 Å2 / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.68-1.723.70.5411.41944652730.541100
1.72-1.773.70.471.61886951290.47100
1.77-1.823.70.4041.91844549920.404100
1.82-1.883.70.3412.21793848570.341100
1.88-1.943.70.3022.51750247370.302100
1.94-2.013.70.2431687945620.24100
2.01-2.083.70.2063.61641644320.20699.9
2.08-2.173.70.1764.21575442560.17699.9
2.17-2.273.70.1554.71509940760.15599.9
2.27-2.383.70.14451457939100.14499.8
2.38-2.53.70.135.51376937180.1399.8
2.5-2.663.70.1235.61314235340.12399.7
2.66-2.843.70.1175.81223233110.11799.5
2.84-3.073.70.1026.31140830900.10299.4
3.07-3.363.70.0847.51051528480.08499.2
3.36-3.763.70.079948825700.0798.9
3.76-4.343.70.0639.6844222870.06398.6
4.34-5.313.70.0659.2718219460.06598.4
5.31-7.513.60.0738.7552815210.07397.5
7.51-29.373.40.0631029438540.06394.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.68→29.374 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 3.519 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.085
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 ATOMS (MG) AND POLYETHYLENE GLYCOL (PEG) FROM THE CRYSTALLIZATION SOLUTION ARE MODELED INTO THE STRUCTURE. 5. TLS PARAMETERS WERE ASSIGNED WITH THE AID OF THE TLS MOTION DETERMINATION SERVER. 6. A RAMACHANDRAN OUTLIER (A106) IS SUPPORTED BY CLEARLY DEFINED DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.182 3624 5 %RANDOM
Rwork0.15 ---
obs0.152 71861 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 50.09 Å2 / Biso mean: 10.511 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.68→29.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4063 0 23 818 4904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224408
X-RAY DIFFRACTIONr_bond_other_d0.0010.023071
X-RAY DIFFRACTIONr_angle_refined_deg1.631.965982
X-RAY DIFFRACTIONr_angle_other_deg0.92737521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.285600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67624.931217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25215787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6571527
X-RAY DIFFRACTIONr_chiral_restr0.0870.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215080
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02893
X-RAY DIFFRACTIONr_mcbond_it0.5131.52729
X-RAY DIFFRACTIONr_mcbond_other0.1571.51136
X-RAY DIFFRACTIONr_mcangle_it0.91824392
X-RAY DIFFRACTIONr_scbond_it1.74231679
X-RAY DIFFRACTIONr_scangle_it2.8754.51555
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1540MEDIUM POSITIONAL0.10.5
2B1875LOOSE POSITIONAL0.255
1A1540MEDIUM THERMAL0.92
2B1875LOOSE THERMAL1.0210
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 258 -
Rwork0.225 5006 -
all-5264 -
obs--99.77 %
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)
10.29240.0845-0.11590.4607-0.1670.5825-0.03280.0236-0.0123-0.07090.0097-0.0358-0.02510.01550.02310.0204-0.00340.00810.0118-0.00380.024155.128281.921879.067
20.4912-0.0153-0.04390.3498-0.02690.31980-0.0085-0.02890.0266-0.00210.00770.016-0.01190.0020.01130.00580.00120.0088-0.00210.005538.773963.9193104.8613
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A48 - 312
2X-RAY DIFFRACTION2B48 - 312

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