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- PDB-4gwg: Crystal Structure Analysis of 6-phosphogluconate dehydrogenase ap... -

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Basic information

Entry
Database: PDB / ID: 4gwg
TitleCrystal Structure Analysis of 6-phosphogluconate dehydrogenase apo-form
Components6-phosphogluconate dehydrogenase, decarboxylating
KeywordsOXIDOREDUCTASE / 6-phosphoglyconate dehydrogenase / dehydrogenase / NADP
Function / homology
Function and homology information


D-gluconate catabolic process / phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / pentose biosynthetic process / pentose-phosphate shunt, oxidative branch / Pentose phosphate pathway / pentose-phosphate shunt / NFE2L2 regulates pentose phosphate pathway genes / NADP binding / extracellular exosome ...D-gluconate catabolic process / phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / pentose biosynthetic process / pentose-phosphate shunt, oxidative branch / Pentose phosphate pathway / pentose-phosphate shunt / NFE2L2 regulates pentose phosphate pathway genes / NADP binding / extracellular exosome / nucleus / cytosol
Similarity search - Function
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 ...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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
6-phosphogluconate dehydrogenase, decarboxylating
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3907 Å
AuthorsHe, C. / Zhou, L. / Zhang, L.
CitationJournal: Cancer Cell / Year: 2012
Title: Phosphoglycerate mutase 1 coordinates glycolysis and biosynthesis to promote tumor growth.
Authors: Hitosugi, T. / Zhou, L. / Elf, S. / Fan, J. / Kang, H.B. / Seo, J.H. / Shan, C. / Dai, Q. / Zhang, L. / Xie, J. / Gu, T.L. / Jin, P. / Aleckovic, M. / Leroy, G. / Kang, Y. / Sudderth, J.A. / ...Authors: Hitosugi, T. / Zhou, L. / Elf, S. / Fan, J. / Kang, H.B. / Seo, J.H. / Shan, C. / Dai, Q. / Zhang, L. / Xie, J. / Gu, T.L. / Jin, P. / Aleckovic, M. / Leroy, G. / Kang, Y. / Sudderth, J.A. / Deberardinis, R.J. / Luan, C.H. / Chen, G.Z. / Muller, S. / Shin, D.M. / Owonikoko, T.K. / Lonial, S. / Arellano, M.L. / Khoury, H.J. / Khuri, F.R. / Lee, B.H. / Ye, K. / Boggon, T.J. / Kang, S. / He, C. / Chen, J.
History
DepositionSep 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Data collection
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: 6-phosphogluconate dehydrogenase, decarboxylating
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6653
Polymers53,2751
Non-polymers3902
Water10,449580
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 6-phosphogluconate dehydrogenase, decarboxylating
hetero molecules

A: 6-phosphogluconate dehydrogenase, decarboxylating
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,3316
Polymers106,5502
Non-polymers7814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10270 Å2
ΔGint-77 kcal/mol
Surface area33480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.280, 87.280, 130.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1170-

HOH

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Components

#1: Protein 6-phosphogluconate dehydrogenase, decarboxylating /


Mass: 53274.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGD, PGDH / Production host: Escherichia coli (E. coli)
References: UniProt: P52209, phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating)
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 580 / 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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 14% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2011
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.3907→30 Å / Num. all: 101681 / Num. obs: 99063 / % possible obs: 97.4 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FWN

3fwn


Resolution: 1.3907→29.091 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.965 / SU ML: 0.16 / σ(F): 1.23 / Phase error: 16.76 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rfree0.1857 9421 5.01 %
Rwork0.1687 --
obs0.1696 188164 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.547 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7744 Å2-0 Å20 Å2
2---0.7744 Å2-0 Å2
3---1.5487 Å2
Refinement stepCycle: LAST / Resolution: 1.3907→29.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3624 0 24 580 4228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053808
X-RAY DIFFRACTIONf_angle_d1.025152
X-RAY DIFFRACTIONf_dihedral_angle_d12.5841432
X-RAY DIFFRACTIONf_chiral_restr0.071557
X-RAY DIFFRACTIONf_plane_restr0.004663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3907-1.40650.23613190.2216000X-RAY DIFFRACTION98
1.4065-1.42310.23723260.21556114X-RAY DIFFRACTION100
1.4231-1.44040.21522890.2036192X-RAY DIFFRACTION100
1.4404-1.45860.21313390.20276146X-RAY DIFFRACTION100
1.4586-1.47780.20213380.1916144X-RAY DIFFRACTION100
1.4778-1.49810.22192950.18526157X-RAY DIFFRACTION100
1.4981-1.51950.19833520.17776103X-RAY DIFFRACTION100
1.5195-1.54220.18563410.17846148X-RAY DIFFRACTION100
1.5422-1.56630.20473410.17686108X-RAY DIFFRACTION100
1.5663-1.59190.18212920.16746186X-RAY DIFFRACTION100
1.5919-1.61940.19593210.1626155X-RAY DIFFRACTION100
1.6194-1.64880.1723100.16346156X-RAY DIFFRACTION100
1.6488-1.68050.19613300.15726141X-RAY DIFFRACTION100
1.6805-1.71480.2053040.15776189X-RAY DIFFRACTION100
1.7148-1.75210.17323360.16166097X-RAY DIFFRACTION100
1.7521-1.79290.1793110.16096164X-RAY DIFFRACTION100
1.7929-1.83770.17933580.16026123X-RAY DIFFRACTION100
1.8377-1.88740.18642980.15296163X-RAY DIFFRACTION100
1.8874-1.94290.24562510.19065013X-RAY DIFFRACTION81
1.9429-2.00560.17643020.15866136X-RAY DIFFRACTION100
2.0056-2.07730.19253230.15536199X-RAY DIFFRACTION100
2.0773-2.16040.18423150.15576116X-RAY DIFFRACTION100
2.1604-2.25870.16942650.17314667X-RAY DIFFRACTION77
2.2587-2.37770.19362710.1634922X-RAY DIFFRACTION80
2.3777-2.52660.18532910.1656155X-RAY DIFFRACTION100
2.5266-2.72160.15693470.16676123X-RAY DIFFRACTION100
2.7216-2.99520.17093540.16626123X-RAY DIFFRACTION100
2.9952-3.4280.17693340.15666132X-RAY DIFFRACTION100
3.428-4.31670.16252490.14694525X-RAY DIFFRACTION74
4.3167-29.09690.17253190.16356146X-RAY DIFFRACTION100

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