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Entry
Database: PDB / ID: 3ktc
TitleCrystal structure of Putative sugar isomerase (YP_050048.1) from ERWINIA CAROTOVORA ATROSEPTICA SCRI1043 at 1.54 A resolution
ComponentsXylose isomerase
KeywordsISOMERASE / Putative sugar isomerase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Carbohydrate metabolism / Metal-binding / Pentose shunt / Xylose metabolism
Function / homology
Function and homology information


D-apiose isomerase / xylose isomerase activity / carbohydrate metabolic process / metal ion binding / cytoplasm
Similarity search - Function
: / Xylose isomerase / Xylose isomerase family profile. / 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
: / Unknown ligand / D-apiose isomerase
Similarity search - Component
Biological speciesPectobacterium atrosepticum SCRI1043 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.54 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative sugar isomerase (YP_050048.1) from ERWINIA CAROTOVORA ATROSEPTICA SCRI1043 at 1.54 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 24, 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: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / 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_asym_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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 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: Xylose isomerase
B: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,26828
Polymers74,9952
Non-polymers1,27426
Water12,773709
1
A: Xylose isomerase
B: Xylose isomerase
hetero molecules

A: Xylose isomerase
B: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,53756
Polymers149,9894
Non-polymers2,54852
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area31220 Å2
ΔGint-144 kcal/mol
Surface area38000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.653, 79.653, 194.406
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-338-

UNL

21A-338-

UNL

31B-363-

HOH

41B-405-

HOH

DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Xylose isomerase


Mass: 37497.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum SCRI1043 (bacteria)
Gene: ECA1953 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q6D5T7, xylose isomerase

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Non-polymers , 6 types, 735 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 3 / Source method: obtained synthetically
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 709 / Source method: isolated from a natural source / Formula: H2O

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Details

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.

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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: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2000M MgCl2, 10.0000% PEG-8000, 0.1M TRIS pH 7.0, 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: 0.91837,0.97855,0.97799
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 16, 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
20.978551
30.977991
ReflectionResolution: 1.54→29.323 Å / Num. obs: 106036 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.505 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.56
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.54-1.60.8581.68305821139195
1.6-1.660.6662.17571519019199.2
1.66-1.730.5122.87566318963199.3
1.73-1.830.373.88892622255199.4
1.83-1.940.2575.57855019594199.5
1.94-2.090.1618.58229620497199.7
2.09-2.30.10113.28228520441199.8
2.3-2.630.07716.98212420326199.8
2.63-3.310.04626.38335220550199.9
3.31-29.3230.02643.98388020648199.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.54→29.323 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.28 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.062
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.MG IONS, CHLORIDE IONS FROM CRYSTALLIZATION AND ETHYLENE GLYCOL FROM CRYOPROTECTANT ARE MODELED IN THE STRUCTURE, RESPECTIVELY. 5.FE IONS WITH 0.80 OCCUPANCY ARE MODELED IN EACH CONSERVED ACTIVE SITE. THE PRESENCE OF FE ATOMS ARE SUPPORTED BY X-RAY FLUORESCENCE MEASUREMENTS. AN UNKNOWN LIGAND(UNL) IS MODELED IN EACH ACTIVE SITE NEAR FE ATOM. 6.ANOTHER UNKNOWN LIGAND (UNL) IS ALSO MODELED NEAR RESIDUE 301 IN SUBUNIT A, WHICH RESEMBLES A BENZOIC ACID FROM BACTERIAL NATURAL PROCESSING.
RfactorNum. reflection% reflectionSelection details
Rfree0.157 5292 5 %RANDOM
Rwork0.136 ---
obs0.137 105995 99.29 %-
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: 68.88 Å2 / Biso mean: 27.172 Å2 / Biso min: 10.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.54→29.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5217 0 95 709 6021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225840
X-RAY DIFFRACTIONr_bond_other_d0.0030.023926
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9467987
X-RAY DIFFRACTIONr_angle_other_deg1.0639552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2735751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63324.315292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.93515917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2031537
X-RAY DIFFRACTIONr_chiral_restr0.0940.2835
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026842
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021253
X-RAY DIFFRACTIONr_nbd_refined0.2360.31304
X-RAY DIFFRACTIONr_nbd_other0.1890.34537
X-RAY DIFFRACTIONr_nbtor_refined0.1870.53012
X-RAY DIFFRACTIONr_nbtor_other0.0880.52934
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.5958
X-RAY DIFFRACTIONr_metal_ion_refined0.220.55
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.348
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2610.3144
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.591
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1460.52
X-RAY DIFFRACTIONr_mcbond_it1.59333808
X-RAY DIFFRACTIONr_mcbond_other0.37731437
X-RAY DIFFRACTIONr_mcangle_it2.06955774
X-RAY DIFFRACTIONr_scbond_it3.57382541
X-RAY DIFFRACTIONr_scangle_it4.948112213
LS refinement shellResolution: 1.539→1.579 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 370 -
Rwork0.206 7208 -
all-7578 -
obs--96.63 %
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)
10.728-0.0899-0.3160.26820.0050.49370.02310.10690.1473-0.04040.03560.0303-0.1413-0.0946-0.0588-0.10080.013-0.0064-0.12080.0289-0.1272-11.321224.227715.3891
20.5583-0.0295-0.17950.3314-0.02440.4939-0.05230.0102-0.0925-0.01950.01710.01380.0786-0.08580.0352-0.1522-0.02890.0041-0.1429-0.0071-0.1354-13.3961-8.495825.982
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 331
2X-RAY DIFFRACTION2B2 - 331

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