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- PDB-1dxi: STRUCTURE DETERMINATION OF GLUCOSE ISOMERASE FROM STREPTOMYCES MU... -

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Basic information

Entry
Database: PDB / ID: 1dxi
TitleSTRUCTURE DETERMINATION OF GLUCOSE ISOMERASE FROM STREPTOMYCES MURINUS AT 2.6 ANGSTROMS RESOLUTION
ComponentsD-XYLOSE ISOMERASE
KeywordsISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
Function / homology
Function and homology information


xylose isomerase / xylose isomerase activity / D-xylose metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
Xylose isomerase, actinobacteria / 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
Biological speciesStreptomyces murinus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsRasmussen, H. / La Cour, T. / Nyborg, J. / Schulein, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Structure determination of glucose isomerase from Streptomyces murinus at 2.6 A resolution.
Authors: Rasmussen, H. / la Cour, T. / Nyborg, J. / Schulein, M.
History
DepositionSep 30, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE SHEETS PRESENTED AS *BA* AND *BB* ON SHEET RECORDS BELOW ARE ACTUALLY TWO EIGHT-STRANDED ...SHEET THE SHEETS PRESENTED AS *BA* AND *BB* ON SHEET RECORDS BELOW ARE ACTUALLY TWO EIGHT-STRANDED BETA-BARRELS. THIS IS REPRESENTED BY TWO NINE-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-XYLOSE ISOMERASE
B: D-XYLOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7436
Polymers85,6462
Non-polymers974
Water724
1
A: D-XYLOSE ISOMERASE
B: D-XYLOSE ISOMERASE
hetero molecules

A: D-XYLOSE ISOMERASE
B: D-XYLOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,48612
Polymers171,2914
Non-polymers1948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area30800 Å2
ΔGint-160 kcal/mol
Surface area47660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)137.650, 137.650, 132.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: CIS PROLINE - PRO A 187 / 2: CIS PROLINE - PRO B 187
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.897, -0.101, -0.43), (-0.104, -0.899, 0.426), (-0.43, 0.427, 0.796)
Vector: 69.239, 69.25, 0.177)

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Components

#1: Protein D-XYLOSE ISOMERASE


Mass: 42822.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces murinus (bacteria) / References: UniProt: P37031, xylose isomerase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.34 %
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlGI solution1drop
20.4 Mammonium sulphate1drop
350 mMmagnesium sulfate1drop
52.0 Mammonium sulfate1reservoir
4Tris-HCl1drop
6Tris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Num. obs: 31564 / % possible obs: 85 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.095

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.6→6 Å / σ(F): 3
Details: FOUR WATER MOLECULES CONNECTED TO THE CATALYTIC SITES HAVE BEEN INCLUDED IN THE STRUCTURE.
RfactorNum. reflection
obs0.214 28032
Refinement stepCycle: LAST / Resolution: 2.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6046 0 4 4 6054
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0460.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0720.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1431.5
X-RAY DIFFRACTIONp_mcangle_it1.7372
X-RAY DIFFRACTIONp_scbond_it2.0482
X-RAY DIFFRACTIONp_scangle_it2.9553
X-RAY DIFFRACTIONp_plane_restr0.0280.02
X-RAY DIFFRACTIONp_chiral_restr0.2810.12
X-RAY DIFFRACTIONp_singtor_nbd0.2060.2
X-RAY DIFFRACTIONp_multtor_nbd0.260.2
X-RAY DIFFRACTIONp_xhyhbond_nbd00.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.0843
X-RAY DIFFRACTIONp_staggered_tor26.38115
X-RAY DIFFRACTIONp_orthonormal_tor35.96345
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 6 Å / Num. reflection obs: 28032 / σ(F): 3 / Rfactor obs: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS

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