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- PDB-6oqz: Crystal structure of Glucose Isomerase from Non-merohedrally twin... -

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Basic information

Entry
Database: PDB / ID: 6oqz
TitleCrystal structure of Glucose Isomerase from Non-merohedrally twinned crystals
ComponentsXylose isomerase
KeywordsISOMERASE / Nonmerohedral twinning / twinned structure solution / twinned structure refinement
Function / homology
Function and homology information


xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein 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
: / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.6 Å
AuthorsSevvana, M. / Ruf, M. / Uson, I. / Sheldrick, G.M. / Herbst-Irmer, R.
Funding support Spain, European Union, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBIO2015-64216-P Spain
European Union (EU)MDM2014-0435European Union
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Non-merohedral twinning: from minerals to proteins.
Authors: Sevvana, M. / Ruf, M. / Uson, I. / Sheldrick, G.M. / Herbst-Irmer, R.
History
DepositionApr 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_label_atom_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

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Assembly

Deposited unit
A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3475
Polymers43,0951
Non-polymers2524
Water5,116284
1
A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,39020
Polymers172,3804
Non-polymers1,00916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area33380 Å2
ΔGint-252 kcal/mol
Surface area44990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.931, 97.935, 102.706
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

21A-672-

HOH

31A-740-

HOH

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Components

#1: Protein Xylose isomerase


Mass: 43095.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05 mM TrisHCl buffer pH 7.5, 0.1 M MnCl2 and 14% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Dec 25, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→70.88 Å / Num. obs: 61943 / % possible obs: 99.9 % / Redundancy: 1 % / Rsym value: 0.032 / Net I/σ(I): 27.01 / Num. measured all: 125668
Reflection shellResolution: 1.6→1.62 Å / Redundancy: 1 % / Mean I/σ(I) obs: 3.93 / Num. unique obs: 2184 / Rsym value: 0.274 / % possible all: 98.1

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Processing

Software
NameClassification
SHELXrefinement
SAINTdata reduction
SADABSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→70.88 Å / Cross valid method: FREE R-VALUE / σ(F): 3
Details: NON-MEROHEDRAL TWIN REFINEMENT AGAINST HKLF4 (DETWINNED DATA)
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3101 5 %THIN SHELLS
Rwork0.19 ---
obs0.19 61943 98.5 %-
all-61943 --
Displacement parametersBiso max: 87.69 Å2 / Biso mean: 16.5733 Å2 / Biso min: 5 Å2
Refinement stepCycle: final / Resolution: 1.6→70.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3041 0 11 284 3336
Biso mean--22.92 23.56 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d1.82
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.46
X-RAY DIFFRACTIONs_zero_chiral_vol0.046
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.053
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.014
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.056
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.6→1.66 Å /
RfactorNum. reflection
Rwork0.241 6188

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