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- PDB-1xlm: D254E, D256E MUTANT OF D-XYLOSE ISOMERASE COMPLEXED WITH AL3 AND ... -

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Basic information

Entry
Database: PDB / ID: 1xlm
TitleD254E, D256E MUTANT OF D-XYLOSE ISOMERASE COMPLEXED WITH AL3 AND XYLITOL
ComponentsD-XYLOSE ISOMERASE
KeywordsISOMERASE / AL / SUBSTRATE INDUCED METAL ION MOVEMENT / XYLOSE METABOLISM / PENTOSE SHUNT
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
ALUMINUM ION / Xylitol / Xylose isomerase
Similarity search - Component
Biological speciesArthrobacter sp. NRRL (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGerczei, T. / Bocskei, Z.S. / Szabo, E. / Naray-Szabo, G. / Asboth, B.
Citation
Journal: Int.J.Biol.Macromol. / Year: 1999
Title: Structure determination and refinement of the Al3+ complex of the D254,256E mutant of Arthrobacter D-xylose isomerase at 2.40 A resolution. Further evidence for inhibitor-induced metal ion movement.
Authors: Gerczei, T. / Bocskei, Z. / Szabo, E. / Asboth, B. / Naray-Szabo, G.
#1: Journal: Proteins / Year: 1997
Title: Role of Electrostatics at the Catalytic Metal Binding Site in Xylose Isomerase Action: Ca(2+)-Inhibition and Metal Competence in the Double Mutant D254E/D256E
Authors: Fuxreiter, M. / Bocskei, Z. / Szeibert, A. / Szabo, E. / Dallmann, G. / Naray-Szabo, G. / Asboth, B.
History
DepositionJul 22, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / software / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _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 / _software.name / _struct_conn.pdbx_dist_value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,8878
Polymers86,4742
Non-polymers4126
Water1,60389
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)173,77316
Polymers172,9494
Non-polymers82412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
Buried area33730 Å2
ΔGint-187 kcal/mol
Surface area44850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)139.600, 140.700, 83.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.076426, -0.997075, -0.001045), (-0.997075, -0.076425, -0.001081), (0.000998, 0.001125, -0.999999)
Vector: 67.2615, 72.6074, 7.5022)

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Components

#1: Protein D-XYLOSE ISOMERASE


Mass: 43237.219 Da / Num. of mol.: 2 / Mutation: D254E, D256E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. NRRL (bacteria) / Strain: B3728 / Plasmid: PAXI3 / Cellular location (production host): SECRETION / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P12070, xylose isomerase
#2: Sugar ChemComp-XYL / Xylitol / D-Xylitol


Type: D-saccharide / Mass: 152.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O5
#3: Chemical
ChemComp-AL / ALUMINUM ION


Mass: 26.982 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Al
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 53 %
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 0.75 M (NH4)2SO4, 1.50 MM THYMOL, 0.05 TRIS, PH 7.0, THEN SOAKED INTO A SOLUTION CONTAINING 5 MM AL3+, 1.5 M XYLITOL, 1.50 M (NH4)2SO4 AND 6.0 M THYMOL IN 1.50 ...Details: PROTEIN WAS CRYSTALLIZED FROM 0.75 M (NH4)2SO4, 1.50 MM THYMOL, 0.05 TRIS, PH 7.0, THEN SOAKED INTO A SOLUTION CONTAINING 5 MM AL3+, 1.5 M XYLITOL, 1.50 M (NH4)2SO4 AND 6.0 M THYMOL IN 1.50 M TRIS-HCL PH 8.0 FOR TWO DAYS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110.0 mg/mlprotein1drop
20.05 MTris1drop
30.75 Mammonium sulfate1drop
41.50 mMthymol1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 1996 / Details: NORMAL FOCUS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→8 Å / Num. obs: 32570 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.078 / Net I/σ(I): 4.87
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 2.65 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.1 / Rsym value: 0.164 / % possible all: 98
Reflection
*PLUS
Num. measured all: 142427 / Rmerge(I) obs: 0.1195

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
bioteXdata reduction
bioteXdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XLA

1xla


Resolution: 2.4→8 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3145 10 %RANDOM
Rwork0.1792 ---
obs0.1792 27301 97.1 %-
Displacement parametersBiso mean: 14.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.252 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.273 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6092 0 24 89 6205
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.07
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.4491.5
X-RAY DIFFRACTIONx_mcangle_it1.132
X-RAY DIFFRACTIONx_scbond_it1.4492
X-RAY DIFFRACTIONx_scangle_it1.132.5
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev Biso : 1.317 Å2 / Rms dev position: 0.017 Å / Weight Biso : 1 / Weight position: 100
LS refinement shellResolution: 2.4→2.44 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 76 10.8 %
Rwork0.235 629 -
obs--45.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2XYL.PARTOPH19.SOL
X-RAY DIFFRACTION3AL.PARXYL.TOP
X-RAY DIFFRACTION4PARAM19.SOLAL.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2223 / Num. reflection obs: 108813
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 13.45 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.07

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