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- PDB-2gyi: DESIGN, SYNTHESIS, AND CHARACTERIZATION OF A POTENT XYLOSE ISOMER... -

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Basic information

Entry
Database: PDB / ID: 2gyi
TitleDESIGN, SYNTHESIS, AND CHARACTERIZATION OF A POTENT XYLOSE ISOMERASE INHIBITOR, D-THREONOHYDROXAMIC ACID, AND HIGH-RESOLUTION X-RAY CRYSTALLOGRAPHIC STRUCTURE OF THE ENZYME-INHIBITOR COMPLEX
ComponentsXYLOSE 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
2,3,4,N-TETRAHYDROXY-BUTYRIMIDIC ACID / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces olivochromogenes (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsAllen, K.N. / Lavie, A. / Petsko, G.A. / Ringe, D.
Citation
Journal: Biochemistry / Year: 1995
Title: Design, Synthesis, and Characterization of a Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-Ray Crystallographic Structure of the Enzyme-Inhibitor Complex
Authors: Allen, K.N. / Lavie, A. / Petsko, G.A. / Ringe, D.
#1: Journal: Biochemistry / Year: 1994
Title: Isotopic Exchange Plus Substrate and Inhibition Kinetics of D-Xylose Isomerase Do not Support a Proton-Transfer Mechanism
Authors: Allen, K.N. / Lavie, A. / Farber, G.K. / Glasfeld, A. / Petsko, G.A. / Ringe, D.
#2: Journal: Biochemistry / Year: 1994
Title: Role of the Divalent Metal Ion in Sugar Binding, Ring Opening, and Isomerization by D-Xylose Isomerase: Replacement of a Catalytic Metal by an Amino Acid
Authors: Allen, K.N. / Lavie, A. / Glasfeld, A. / Tanada, T.N. / Gerrity, D.P. / Carlson, S.C. / Farber, G.K. / Petsko, G.A. / Ringe, D.
#3: Journal: Biochemistry / Year: 1994
Title: X-Ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence for Metal Movement During Catalysis
Authors: Lavie, A. / Allen, K.N. / Petsko, G.A. / Ringe, D.
History
DepositionSep 1, 1994Processing site: BNL
SupersessionJul 10, 1995ID: 1GYI
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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 *S1* AND *S2* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA- ...SHEET THE SHEETS PRESENTED AS *S1* AND *S2* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. THIS IS REPRESENTED BY NINE-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS OF EACH ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,0898
Polymers85,6902
Non-polymers3996
Water11,422634
1
A: XYLOSE ISOMERASE
B: XYLOSE ISOMERASE
hetero molecules

A: XYLOSE ISOMERASE
B: XYLOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,17816
Polymers171,3794
Non-polymers79912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area33080 Å2
ΔGint-185 kcal/mol
Surface area45620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.900, 99.050, 93.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: SER A 63 - ASP A 64 OMEGA = 247.14 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: CIS PROLINE - PRO A 186 / 3: CIS PROLINE - PRO B 186
Components on special symmetry positions
IDModelComponents
11A-1633-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99927, 0.03829, -0.00045), (0.03829, -0.99927, 0.001), (-0.00041, -0.00102, -1)
Vector: -0.02028, 0.02478, -47.31872)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 2 .. A 386 B 2 .. B 386 1.200

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Components

#1: Protein XYLOSE ISOMERASE


Mass: 42844.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces olivochromogenes (bacteria)
References: UniProt: P15587, xylose isomerase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-HYA / 2,3,4,N-TETRAHYDROXY-BUTYRIMIDIC ACID


Mass: 151.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHERE IS ONE D-THREONOHYDROXAMIC ACID MOLECULE BOUND IN THE LINEAR FORM IN THE ACTIVE SITE OF EACH ...THERE IS ONE D-THREONOHYDROXAMIC ACID MOLECULE BOUND IN THE LINEAR FORM IN THE ACTIVE SITE OF EACH MONOMER. IT IS LABELED HYA A 960 IN MONOMER 1 AND HYA B 970 IN MONOMER 2. THERE ARE TWO WATER MOLECULES IN THE ACTIVE SITE OF EACH MONOMER MAKING A LIGAND TO MAGNESIUM, NUMBERED HOH 1700 AND 1701 IN MONOMER 1 AND HOH 1800 AND 1801 IN MONOMER 2.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
143 mg/mlenzyme1drop
20.025 MPIPES1drop
30.010 M1dropMgCl2
40.001 M1dropCaCl2
545 %satammonium sulfate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 44.72 Å / Num. obs: 83616 / Num. measured all: 190809 / Rmerge(I) obs: 0.051

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.6→10 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.216 -
obs0.216 83228
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6036 0 24 634 6694
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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