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- PDB-1xru: Crystal Structure of 5-keto-4-deoxyuronate Isomerase from Escheri... -

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Basic information

Entry
Database: PDB / ID: 1xru
TitleCrystal Structure of 5-keto-4-deoxyuronate Isomerase from Eschericia coli
Components4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
KeywordsISOMERASE / BETA BARREL / CUPIN
Function / homology
Function and homology information


5-dehydro-4-deoxy-D-glucuronate isomerase / 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase activity / D-galacturonate catabolic process / D-glucuronate catabolic process / glucose-6-phosphate isomerase activity / pectin catabolic process / protein homodimerization activity / zinc ion binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
pectin degrading enzyme 5-keto 4- deoxyuronate isomerase, domain 1 / 5-keto 4-deoxyuronate isomerase / 5-keto-4-deoxyuronate isomerase, N-terminal / KduI/IolB isomerase / KduI/IolB family / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.94 Å
AuthorsCrowther, R.L. / Georgiadis, M.M.
CitationJournal: Proteins / Year: 2005
Title: The crystal structure of 5-keto-4-deoxyuronate isomerase from Escherichia coli
Authors: Crowther, R.L. / Georgiadis, M.M.
History
DepositionOct 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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_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.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
Remark 999SEQUENCE Author states that the C-terminal differences from database sequence is a neutral ...SEQUENCE Author states that the C-terminal differences from database sequence is a neutral designation. The C-terminal sequence reported here is indeed correct for the gene that was cloned and for protein that was crystallized.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
B: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3566
Polymers63,7492
Non-polymers6074
Water8,233457
1
A: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
B: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
hetero molecules

A: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
B: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
hetero molecules

A: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
B: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,06918
Polymers191,2476
Non-polymers1,82212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
MethodPQS
2
A: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
hetero molecules

B: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3566
Polymers63,7492
Non-polymers6074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
Buried area3690 Å2
ΔGint-28 kcal/mol
Surface area21650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.972, 102.972, 176.862
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations: -y, x-y, z and y-x, -x, z.

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Components

#1: Protein 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase / 5-keto-4-deoxyuronate isomerase / DKI isomerase


Mass: 31874.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: kduI / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: Q46938, 5-dehydro-4-deoxy-D-glucuronate isomerase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: PEG 400, calcium chloride, HEPES, pH 7, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.980122, 0.979634, 0.979538
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2002
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9801221
20.9796341
30.9795381
ReflectionResolution: 1.94→50 Å / Num. all: 51624 / Num. obs: 51573 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rsym value: 0.07 / Net I/σ(I): 9
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 5124 / Rsym value: 0.2 / % possible all: 99.3

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.94→12.97 Å / Isotropic thermal model: OVERALL / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.191 2562 -RANDOM
Rwork0.164 ---
all0.165 51768 --
obs0.165 51449 99.4 %-
Displacement parametersBiso mean: 16.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.61 Å20 Å2
2--0.21 Å20 Å2
3----0.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.94→12.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4374 0 34 457 4865
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3

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