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- PDB-1xyc: X-RAY CRYSTALLOGRAPHIC STRUCTURES OF D-XYLOSE ISOMERASE-SUBSTRATE... -

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Basic information

Entry
Database: PDB / ID: 1xyc
TitleX-RAY CRYSTALLOGRAPHIC STRUCTURES OF D-XYLOSE ISOMERASE-SUBSTRATE COMPLEXES POSITION THE SUBSTRATE AND PROVIDE EVIDENCE FOR METAL MOVEMENT DURING CATALYSIS
ComponentsXYLOSE ISOMERASE
KeywordsISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
Function / homology
Function and homology information


xylose isomerase / D-xylose metabolic process / xylose isomerase activity / 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
3-O-METHYLFRUCTOSE IN LINEAR FORM / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces olivochromogenes (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.19 Å
AuthorsLavie, A. / Allen, K.N. / Petsko, G.A. / Ringe, D.
Citation
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.
#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: The 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.
History
DepositionJan 3, 1994Processing site: BNL
Revision 1.0May 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 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 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.ptnr2_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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 *SA1*, *SA2*, *SB1*, AND *SB2* ON SHEET RECORDS BELOW ARE ACTUALLY ...SHEET THE SHEETS PRESENTED AS *SA1*, *SA2*, *SB1*, AND *SB2* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. THESE ARE REPRESENTED AS NINE-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS OF EACH SHEET ARE IDENTICAL. THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS *SA1* AND *SB1* REPRESENT ONE BIFURCATED SHEET. SHEETS *SA2* AND *SB2* REPRESENT ANOTHER BIFURCATED SHEET.

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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)86,1758
Polymers85,6902
Non-polymers4866
Water8,107450
1
A: XYLOSE ISOMERASE
B: XYLOSE ISOMERASE
hetero molecules

A: XYLOSE ISOMERASE
B: XYLOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,35116
Polymers171,3794
Non-polymers97112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area33430 Å2
ΔGint-184 kcal/mol
Surface area45130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)87.700, 99.300, 94.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: CIS PROLINE - PRO A 186 / 2: CIS PROLINE - PRO B 686
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)

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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: Sugar ChemComp-3MF / 3-O-METHYLFRUCTOSE IN LINEAR FORM


Type: saccharide / Mass: 194.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHERE IS ONE SUGAR MOLECULE IN THE OPEN FORM BOUND TO THE ENZYME IN EACH ACTIVE SITE. THE SUGAR WAS ...THERE IS ONE SUGAR MOLECULE IN THE OPEN FORM BOUND TO THE ENZYME IN EACH ACTIVE SITE. THE SUGAR WAS MODELED AS 3-O-METHYLFRUCTOSE (LABELED 3MF A 950 IN MONOMER 1 AND 3MF B 960 IN MONOMER 2) BUT AT THIS RESOLUTION IT IS HARD TO DISTINGUISH BETWEEN THE ABOVE AND 3-O-METHYLGLUCOSE. THE ELECTRON DENSITY SEEN PROBABLY REPRESENTS A MIXTURE OF THE REACTION SUBSTRATE AND PRODUCT.
Sequence detailsTHE SEQUENCE REPORTED HERE DISAGREES WITH THAT ORIGINALLY REPORTED (FARBER ET AL., BIOCHEMISTRY V. ...THE SEQUENCE REPORTED HERE DISAGREES WITH THAT ORIGINALLY REPORTED (FARBER ET AL., BIOCHEMISTRY V. 28, P. 7289, 1989) AND FOUND AS SWISS-PROT: XYLA_STROL AND PIR: S28986. A TOTAL OF 13 AMINO ACIDS WERE CHANGED, OF WHICH 5 WERE IN THE C-TERMINAL DOMAIN. THE AUTHORS STATE THAT THIS CORRECTED SEQUENCE WILL BE INCLUDED IN THE SPRING 1994 RELEASES OF THE SEQUENCE DATA BASES. SEE THE JRNL REFERENCE ABOVE FOR MORE INFORMATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.64 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
145 %satammonium sulfate1reservoir
243 mg/mlenzyme1drop
30.025 MPIPES1drop
40.010 M1dropMgCl2
50.001 M1dropCaCl2

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Data collection

Reflection
*PLUS
Highest resolution: 2.19 Å / Lowest resolution: 9999 Å / Num. obs: 42123 / % possible obs: 98 % / Num. measured all: 417620 / Rmerge(I) obs: 0.043

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.19→10 Å / Rfactor Rwork: 0.159 / Rfactor obs: 0.159
Refinement stepCycle: LAST / Resolution: 2.19→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6048 0 30 450 6528
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
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
Refinement
*PLUS
Rfactor obs: 0.159 / Rfactor Rwork: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d2.7
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg1.1

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