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Basic information

Entry
Database: PDB / ID: 2iz0
TitlePEX inhibitor-home data
Components6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
KeywordsOXIDOREDUCTASE / PENTOSE SHUNT / GLUCONATE UTILIZATION / PENTOSE PHOSPHATE PATHWAY
Function / homology
Function and homology information


phosphogluconate 2-dehydrogenase activity / D-gluconate catabolic process / phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / pentose-phosphate shunt, oxidative branch / NADP binding / cytosol
Similarity search - Function
6-Phosphogluconate Dehydrogenase, domain 3 / 6-phosphogluconate-binding site / 6-phosphogluconate dehydrogenase signature. / 6-phosphogluconate dehydrogenase, decarboxylating / 6-phosphogluconate dehydrogenase, C-terminal / 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase ...6-Phosphogluconate Dehydrogenase, domain 3 / 6-phosphogluconate-binding site / 6-phosphogluconate dehydrogenase signature. / 6-phosphogluconate dehydrogenase, decarboxylating / 6-phosphogluconate dehydrogenase, C-terminal / 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / 4-PHOSPHO-D-ERYTHRONOHYDROXAMIC ACID / 6-phosphogluconate dehydrogenase, decarboxylating
Similarity search - Component
Biological speciesLACTOCOCCUS LACTIS (lactic acid bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSundaramoorthy, R. / Iulek, J. / Hunter, W.N.
CitationJournal: FEBS J. / Year: 2007
Title: Crystal Structures of a Bacterial 6- Phosphogluconate Dehydrogenase Reveal Aspects of Specificity, Mechanism and Mode of Inhibition by Analogues of High-Energy Reaction Intermediates.
Authors: Sundaramoorthy, R. / Iulek, J. / Barrett, M.P. / Bidet, O. / Ruda, G.F. / Gilbert, I.H. / Hunter, W.N.
History
DepositionJul 23, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
B: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
C: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,46817
Polymers158,3333
Non-polymers3,13614
Water29,7611652
1
A: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
B: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,69411
Polymers105,5552
Non-polymers2,1399
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15260 Å2
ΔGint-82 kcal/mol
Surface area33290 Å2
MethodPISA
2
C: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
hetero molecules

C: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,54812
Polymers105,5552
Non-polymers1,99310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14640 Å2
ΔGint-117.1 kcal/mol
Surface area33740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.957, 104.459, 241.478
Angle α, β, γ (deg.)90.00, 98.52, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNVALVALBB5 - 87 - 10
21ASNASNVALVALCC5 - 87 - 10
12VALVALTHRTHRBB22 - 2824 - 30
22VALVALTHRTHRCC22 - 2824 - 30
13LYSLYSGLYGLYBB66 - 13068 - 132
23LYSLYSGLYGLYCC66 - 13068 - 132
14GLYGLYGLYGLYBB137 - 260139 - 262
24GLYGLYGLYGLYCC137 - 260139 - 262
15GLYGLYLYSLYSBB265 - 295267 - 297
25GLYGLYLYSLYSCC265 - 295267 - 297
16PHEPHEILEILEBB312 - 427314 - 429
26PHEPHEILEILECC312 - 427314 - 429
17ALAALAHISHISBB445 - 453447 - 455
27ALAALAHISHISCC445 - 453447 - 455
18HISHISTYRTYRBB465 - 469467 - 471
28HISHISTYRTYRCC465 - 469467 - 471

NCS oper:
IDCodeMatrixVector
1given(0.5986, -0.7652, -0.237), (-0.7613, -0.6355, 0.1288), (-0.2492, 0.1033, -0.9629)27.24, 5.682, 157.7
2given(-0.3628, 0.9129, 0.1871), (-0.9136, -0.388, 0.1215), (0.1836, -0.1269, 0.9748)11.66, 5.619, 79.41

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING


Mass: 52777.508 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOCOCCUS LACTIS (lactic acid bacteria)
Strain: MG1363 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P96789, phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating)

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Non-polymers , 9 types, 1666 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-RES / 4-PHOSPHO-D-ERYTHRONOHYDROXAMIC ACID


Mass: 231.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10NO8P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-ATR / 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1652 / 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: 2.4 Å3/Da / Density % sol: 48 %
Description: DATA WERE COLLECTED USING OSCILLATION PHOTOGRAPH
Crystal growpH: 7.2
Details: 25% PEG 3350, 0.1M SODIUM CACODYLATE PH 6.4, 300MM AMMONIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Apr 22, 2005 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→45 Å / Num. obs: 52468 / % possible obs: 97.5 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 41.7
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 11.2 / % possible all: 83.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→235.7 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.921 / SU B: 13.583 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2659 5.1 %RANDOM
Rwork0.123 ---
obs0.126 49749 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å2-0.48 Å2
2--0.23 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.6→235.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11008 0 192 1652 12852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02211939
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210775
X-RAY DIFFRACTIONr_angle_refined_deg1.1241.98716261
X-RAY DIFFRACTIONr_angle_other_deg0.815325259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.78151548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88324.885563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.146152114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1181563
X-RAY DIFFRACTIONr_chiral_restr0.0710.21777
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213347
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022370
X-RAY DIFFRACTIONr_nbd_refined0.1960.22886
X-RAY DIFFRACTIONr_nbd_other0.1650.211598
X-RAY DIFFRACTIONr_nbtor_refined0.180.25792
X-RAY DIFFRACTIONr_nbtor_other0.0810.27013
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.21522
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1780.2196
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.298
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.60827762
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.948311609
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4034.55276
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.04264573
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 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B2090medium positional0.130.5
2C2090medium positional0.130.5
1B3144loose positional0.315
2C3144loose positional0.315
1B2090medium thermal0.342
2C2090medium thermal0.342
1B3144loose thermal0.7410
2C3144loose thermal0.7410
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.263 194
Rwork0.161 2987
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3814-0.1877-0.28620.71520.49021.34880.0327-0.0157-0.0204-0.1291-0.02610.06350.0893-0.0983-0.0066-0.0626-0.0254-0.0442-0.03440.0256-0.0687-6.72154.663464.0563
21.57381.42860.60922.18850.52022.499-0.0364-0.0095-0.0010.05980.0618-0.134-0.13820.1755-0.0254-0.13420.0496-0.0021-0.1002-0.0277-0.01021.766233.240190.3907
30.5453-0.19480.41050.399-0.17960.79830.0022-0.05080.0282-0.00640.00090.00840.0086-0.0881-0.0031-0.1044-0.00440.0176-0.0427-0.0179-0.04814.097415.959698.5504
41.73490.11670.13141.68530.98393.47490.03250.1206-0.3745-0.1197-0.1440.06410.3016-0.38750.1115-0.0701-0.0916-0.04240.0098-0.0135-0.0222-17.1855-5.673473.5033
50.3024-0.0162-0.21630.5720.24621.1083-0.0295-0.0476-0.020.07840.02590.04350.1320.04510.0037-0.006-0.00590.0059-0.08880.0225-0.0583-3.466-13.207318.2219
62.44320.3901-0.91871.3309-0.20692.6060.01530.09780.1276-0.18630.0007-0.18240.00960.285-0.0160.01460.08030.0501-0.11630.0076-0.015419.8905-20.8883-12.0844
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 427
2X-RAY DIFFRACTION1A1470 - 1474
3X-RAY DIFFRACTION2A431 - 469
4X-RAY DIFFRACTION3B1 - 427
5X-RAY DIFFRACTION3B1470
6X-RAY DIFFRACTION4B431 - 469
7X-RAY DIFFRACTION5C1 - 427
8X-RAY DIFFRACTION5C1470
9X-RAY DIFFRACTION6C431 - 469

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