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- PDB-2xhz: Probing the active site of the sugar isomerase domain from E. col... -

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Basic information

Entry
Database: PDB / ID: 2xhz
TitleProbing the active site of the sugar isomerase domain from E. coli arabinose-5-phosphate isomerase via X-ray crystallography
ComponentsARABINOSE 5-PHOSPHATE ISOMERASE
KeywordsISOMERASE / LIPOPOLYSACCHARIDE BIOGENESIS
Function / homology
Function and homology information


arabinose-5-phosphate isomerase / arabinose-5-phosphate isomerase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / carbohydrate derivative binding / protein homotetramerization / identical protein binding / metal ion binding
Similarity search - Function
Phosphosugar isomerase, KdsD/KpsF-type / : / KpsF-like, SIS domain / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / CBS domain superfamily / CBS domain ...Phosphosugar isomerase, KdsD/KpsF-type / : / KpsF-like, SIS domain / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Arabinose 5-phosphate isomerase KdsD
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGourlay, L.J. / Sommaruga, S. / Nardini, M. / Sperandeo, P. / Deho, G. / Polissi, A. / Bolognesi, M.
CitationJournal: Protein Sci. / Year: 2010
Title: Probing the Active Site of the Sugar Isomerase Domain from E. Coli Arabinose-5-Phosphate Isomerase Via X-Ray Crystallography.
Authors: Gourlay, L.J. / Sommaruga, S. / Nardini, M. / Sperandeo, P. / Deho, G. / Polissi, A. / Bolognesi, M.
History
DepositionJun 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARABINOSE 5-PHOSPHATE ISOMERASE
B: ARABINOSE 5-PHOSPHATE ISOMERASE
C: ARABINOSE 5-PHOSPHATE ISOMERASE
D: ARABINOSE 5-PHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)77,3184
Polymers77,3184
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11760 Å2
ΔGint-98.4 kcal/mol
Surface area24210 Å2
MethodPISA
2
A: ARABINOSE 5-PHOSPHATE ISOMERASE
B: ARABINOSE 5-PHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)38,6592
Polymers38,6592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-38.9 kcal/mol
Surface area13810 Å2
MethodPISA
3
C: ARABINOSE 5-PHOSPHATE ISOMERASE
D: ARABINOSE 5-PHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)38,6592
Polymers38,6592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-36.8 kcal/mol
Surface area13730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.860, 67.430, 82.170
Angle α, β, γ (deg.)90.00, 106.94, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A10 - 183
2114B10 - 183
3114C10 - 183
4114D10 - 183

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Components

#1: Protein
ARABINOSE 5-PHOSPHATE ISOMERASE / KDSD / YRBH


Mass: 19329.508 Da / Num. of mol.: 4 / Fragment: SUGAR ISOMERASE DOMAIN, RESIDUES 1-183 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P45395, arabinose-5-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 1.8 Å3/Da / Density % sol: 32 % / Description: NONE
Crystal growpH: 7.5
Details: 20% PEG-8000 100MM HEPES PH 7.5 (WIZARD I SCREEN,[EMERALD BIOSYSTEMS] CONDITION 21).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 17026 / % possible obs: 94.3 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Biso Wilson estimate: 42.7 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 5.9
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.4 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ETN

3etn


Resolution: 2.6→40 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.858 / SU B: 20.197 / SU ML: 0.409 / Cross valid method: THROUGHOUT / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.30503 863 5.1 %RANDOM
Rwork0.26075 ---
obs0.26302 16148 93.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.384 Å2
Baniso -1Baniso -2Baniso -3
1-5.16 Å20 Å25.24 Å2
2---2.76 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5086 0 0 9 5095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0225172
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.431.977003
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8135689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.86124.138174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6115882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5071524
X-RAY DIFFRACTIONr_chiral_restr0.0310.2838
X-RAY DIFFRACTIONr_gen_planes_refined
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_it0.4431.53434
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8225499
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.71131738
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3624.51504
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1255 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.420.5
2Bmedium positional0.420.5
3Cmedium positional0.390.5
4Dmedium positional0.370.5
1Amedium thermal0.052
2Bmedium thermal0.052
3Cmedium thermal0.052
4Dmedium thermal0.052
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 57 -
Rwork0.362 1235 -
obs--95.56 %

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