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- PDB-4hhm: Crystal structure of a mutant, G219A, of Glucose Isomerase from S... -

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Basic information

Entry
Database: PDB / ID: 4hhm
TitleCrystal structure of a mutant, G219A, of Glucose Isomerase from Streptomyces sp. SK
ComponentsXylose isomerase
KeywordsISOMERASE / TIM-barrel
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
: / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces sp. SK (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBen Hlima, H. / Riguet, J. / Haser, R. / Aghajari, N.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2013
Title: Identification of critical residues for the activity and thermostability of Streptomyces sp. SK glucose isomerase.
Authors: Ben Hlima, H. / Bejar, S. / Riguet, J. / Haser, R. / Aghajari, N.
History
DepositionOct 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Nov 13, 2013Group: Database references
Revision 1.4Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)344,76424
Polymers344,0988
Non-polymers66616
Water42,4612357
1
A: Xylose isomerase
B: Xylose isomerase
C: Xylose isomerase
D: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,38212
Polymers172,0494
Non-polymers3338
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31110 Å2
ΔGint-199 kcal/mol
Surface area46590 Å2
MethodPISA
2
E: Xylose isomerase
F: Xylose isomerase
G: Xylose isomerase
H: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,38212
Polymers172,0494
Non-polymers3338
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31320 Å2
ΔGint-194 kcal/mol
Surface area46450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.500, 137.400, 136.600
Angle α, β, γ (deg.)90.00, 90.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Xylose isomerase


Mass: 43012.234 Da / Num. of mol.: 8 / Mutation: G219A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. SK (bacteria) / Gene: xylA / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZAI3, xylose isomerase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2357 / 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: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: PEG 3350, Mg acetate, pH 7, VAPOR DIFFUSION, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.15→48.5 Å / Num. obs: 163122 / % possible obs: 95.4 % / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Rsym value: 0.073 / Net I/σ(I): 11.7
Reflection shellResolution: 2.15→2.2 Å / % possible all: 86.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MUW

1muw


Resolution: 2.15→48.5 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.25 8172 RANDOM
Rwork0.197 --
obs0.197 163122 -
all-171294 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.624 Å20 Å21.123 Å2
2--14.222 Å20 Å2
3----7.597 Å2
Refinement stepCycle: LAST / Resolution: 2.15→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24184 0 16 2357 26557
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.1631.5
X-RAY DIFFRACTIONc_mcangle_it1.9492
X-RAY DIFFRACTIONc_scbond_it1.9492
X-RAY DIFFRACTIONc_scangle_it2.6932.5
LS refinement shellResolution: 2.15→2.2 Å
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5carbohydrate.param

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