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- PDB-2j0e: Three dimensional structure and catalytic mechanism of 6- phospho... -

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Basic information

Entry
Database: PDB / ID: 2j0e
TitleThree dimensional structure and catalytic mechanism of 6- phosphogluconolactonase from Trypanosoma brucei
Components6-PHOSPHOGLUCONOLACTONASE
KeywordsHYDROLASE / CATALYTIC MECHANISM / PENTOSE PHOSPHATE PATHWAY / 6-PHOSPHOGLUCONOLACTONASE / TRYPANOSOMA BRUCEI / ZINC BINDING SITE
Function / homology
Function and homology information


6-phosphogluconolactonase / 6-phosphogluconolactonase activity / glycosome / pentose-phosphate shunt / carbohydrate metabolic process / metal ion binding / cytoplasm
Similarity search - Function
6-Phosphogluconolactonase / 6-phosphogluconolactonase, DevB-type / Glucosamine/galactosamine-6-phosphate isomerase / Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase / Rossmann fold - #1360 / NagB/RpiA transferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / : / 6-phosphogluconolactonase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsDelarue, M. / Duclert-Savatier, N. / Miclet, E. / Haouz, A. / Giganti, D. / Ouazzani, J. / Lopez, P. / Nilges, M. / Stoven, V.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Three Dimensional Structure and Implications for the Catalytic Mechanism of 6-Phosphogluconolactonase from Trypanosoma Brucei.
Authors: Delarue, M. / Duclert-Savatier, N. / Miclet, E. / Haouz, A. / Giganti, D. / Ouazzani, J. / Lopez, P. / Nilges, M. / Stoven, V.
History
DepositionAug 2, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _struct_conn.pdbx_dist_value / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-PHOSPHOGLUCONOLACTONASE
B: 6-PHOSPHOGLUCONOLACTONASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3329
Polymers57,3602
Non-polymers9727
Water8,305461
1
A: 6-PHOSPHOGLUCONOLACTONASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1464
Polymers28,6801
Non-polymers4673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 6-PHOSPHOGLUCONOLACTONASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1865
Polymers28,6801
Non-polymers5064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.310, 80.850, 90.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9994, -0.0079, -0.0347), (0.0108, 0.9964, 0.0842), (0.0339, -0.0845, 0.9958)
Vector: -0.3937, 14.3518, -46.0985)

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Components

#1: Protein 6-PHOSPHOGLUCONOLACTONASE


Mass: 28679.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ONE BOUND ZINC ATOM PER MONOMER. / Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Plasmid: PET21 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9GRG6, 6-phosphogluconolactonase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.32 Å3/Da / Density % sol: 46 %
Description: ANOTHER DATASET WITH SELENOMETHIONYLATED PROTEIN WAS COLLECTED AT 2.8 ANGSTROM AND WAS USED TO CHECK THE POSITION OF METHIONINES.
Crystal growpH: 7.5
Details: 30% PEG MME, 50MM NA ACETATE, HEPES PH 7.5 100 MM. PROTEIN 10MG/ML

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.008014
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008014 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 57076 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3.84 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.92
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.86 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→18 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE STRUCTURE WAS REFINED ON THE CRYSTAL SOAKED WITH A MERCURY DERIVATIVE (2 HG ATOMS PER MONOMER)
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1539 5.1 %RANDOM
Rwork0.206 ---
obs0.206 30438 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.7024 Å2 / ksol: 0.334866 e/Å3
Displacement parametersBiso mean: 28.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.997 Å20 Å20 Å2
2--2.535 Å20 Å2
3----1.538 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.1→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 7 461 4408
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it3.182.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.282 240 5 %
Rwork0.225 4603 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM

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