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- PDB-4xkm: Crystal structure of Xylose Isomerase from an human intestinal tr... -

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Basic information

Entry
Database: PDB / ID: 4xkm
TitleCrystal structure of Xylose Isomerase from an human intestinal tract microbe Bacteroides thetaiotaomicron
ComponentsXylose isomerase
KeywordsISOMERASE / Xylose Isomerase / Bacteroides thetaiotaomicron
Function / homology
Function and homology information


D-xylose catabolic process / xylose isomerase / xylose isomerase activity / magnesium ion binding / cytoplasm
Similarity search - Function
Xylose isomerase, bacterial-type / 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
: / Xylose isomerase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsHan, B.G. / Bong, S.M. / Cho, J.W. / Lee, B.I.
CitationJournal: Biodesign / Year: 2015
Title: Crystal structure of a class 2 D-xylose isomerase from the human intestinal tract microbe Bacteroides thetaiotaomicron
Authors: Han, B.G. / Bong, S.M. / Cho, J.W. / Kim, M.D. / Kim, S.J. / Lee, B.I.
History
DepositionJan 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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 / pdbx_struct_oper_list / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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

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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
C: Xylose isomerase
D: Xylose isomerase
E: Xylose isomerase
F: Xylose isomerase
G: Xylose isomerase
H: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)410,24224
Polymers409,3638
Non-polymers87916
Water46,8392600
1
A: Xylose isomerase
B: Xylose isomerase
G: Xylose isomerase
H: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,12112
Polymers204,6824
Non-polymers4408
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29040 Å2
ΔGint-101 kcal/mol
Surface area55150 Å2
MethodPISA
2
C: Xylose isomerase
D: Xylose isomerase
E: Xylose isomerase
F: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,12112
Polymers204,6824
Non-polymers4408
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29100 Å2
ΔGint-102 kcal/mol
Surface area55150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.268, 101.658, 108.307
Angle α, β, γ (deg.)82.76, 68.24, 82.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Xylose isomerase /


Mass: 51170.398 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: xylA, BT_0793 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A9M2, xylose isomerase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2600 / 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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium chloride, 100 mM bicine pH9.0, 20%(v/v) polyethylene glycol monomethyl ether 550 (PEG MME 550)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 214399 / % possible obs: 98.3 % / Redundancy: 3.9 % / Net I/σ(I): 19.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PHENIXphasing
HKL-2000data scaling
RefinementResolution: 2.1→38.21 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.512 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21131 9914 5 %RANDOM
Rwork0.18558 ---
obs0.18686 188364 90.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0.1 Å20.48 Å2
2---0.13 Å2-0.06 Å2
3---0.16 Å2
Refinement stepCycle: 1 / Resolution: 2.1→38.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27384 0 16 2600 30000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01927976
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7861.93937672
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.34253472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90925.0281416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.935154848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.415120
X-RAY DIFFRACTIONr_chiral_restr0.0560.23872
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0221648
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2652.3413912
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.4853.50917376
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.2342.35714064
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined2.73420.18548078
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.104→2.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 449 -
Rwork0.217 9113 -
obs--59.08 %

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