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- PDB-6jyu: Crystal structure of Human G6PD Canton -

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Basic information

Entry
Database: PDB / ID: 6jyu
TitleCrystal structure of Human G6PD Canton
ComponentsGlucose-6-phosphate 1-dehydrogenase
KeywordsOXIDOREDUCTASE / G6PD deficiency / Hemolytic anemia / Oxidative stress
Function / homology
Function and homology information


pentose biosynthetic process / ribose phosphate biosynthetic process / response to iron(III) ion / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase (NADP+) / glucose-6-phosphate dehydrogenase activity / Pentose phosphate pathway / pentose-phosphate shunt, oxidative branch / negative regulation of cell growth involved in cardiac muscle cell development / NADPH regeneration ...pentose biosynthetic process / ribose phosphate biosynthetic process / response to iron(III) ion / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase (NADP+) / glucose-6-phosphate dehydrogenase activity / Pentose phosphate pathway / pentose-phosphate shunt, oxidative branch / negative regulation of cell growth involved in cardiac muscle cell development / NADPH regeneration / glucose 6-phosphate metabolic process / NADP+ metabolic process / pentose-phosphate shunt / D-glucose binding / NFE2L2 regulates pentose phosphate pathway genes / response to food / erythrocyte maturation / cholesterol biosynthetic process / negative regulation of reactive oxygen species metabolic process / regulation of neuron apoptotic process / glutathione metabolic process / substantia nigra development / TP53 Regulates Metabolic Genes / lipid metabolic process / centriolar satellite / cytoplasmic side of plasma membrane / glucose metabolic process / NADP binding / cellular response to oxidative stress / response to ethanol / intracellular membrane-bounded organelle / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.89 Å
AuthorsAu, S.W.N.
Citation
Journal: To Be Published
Title: Crystal structure of Human G6PD Canton
Authors: Au, S.W.N.
#1: Journal: Structure / Year: 2000
Title: Human glucose-6-phosphate dehydrogenase: the crystal structure reveals a structural NADP(+) molecule and provides insights into enzyme deficiency
Authors: Au, S.W.N. / Zhang, H. / Sun, K. / Engel, P. / Migaud, M.
History
DepositionApr 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6272
Polymers55,8841
Non-polymers7431
Water11,223623
1
A: Glucose-6-phosphate 1-dehydrogenase
hetero molecules

A: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2544
Polymers111,7672
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area7880 Å2
ΔGint-28 kcal/mol
Surface area38970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.422, 172.830, 215.522
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Space group name HallF22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x,y+1/2,z+1/2
#6: x,-y+1/2,-z+1/2
#7: -x,y+1/2,-z+1/2
#8: -x,-y+1/2,z+1/2
#9: x+1/2,y,z+1/2
#10: x+1/2,-y,-z+1/2
#11: -x+1/2,y,-z+1/2
#12: -x+1/2,-y,z+1/2
#13: x+1/2,y+1/2,z
#14: x+1/2,-y+1/2,-z
#15: -x+1/2,y+1/2,-z
#16: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-708-

HOH

21A-727-

HOH

31A-898-

HOH

41A-969-

HOH

51A-1036-

HOH

61A-1162-

HOH

71A-1321-

HOH

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Components

#1: Protein Glucose-6-phosphate 1-dehydrogenase / G6PD


Mass: 55883.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G6PD / Production host: Escherichia coli (E. coli) / Strain (production host): DF213
References: UniProt: P11413, glucose-6-phosphate dehydrogenase (NADP+)
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris, 20% glycerol ethoxylate, 10% tetrahydrofuran

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.98 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.89→25.21 Å / Num. obs: 45396 / % possible obs: 99.2 % / Redundancy: 5.9 % / Biso Wilson estimate: 19.3 Å2 / Net I/σ(I): 34.25
Reflection shellResolution: 1.9→1.97 Å

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementResolution: 1.89→25.21 Å / SU ML: 0.187 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.8813
RfactorNum. reflection% reflection
Rfree0.1919 2000 4.5 %
Rwork0.1539 --
obs0.1557 44443 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.8 Å2
Refinement stepCycle: LAST / Resolution: 1.89→25.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 48 623 4605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00664082
X-RAY DIFFRACTIONf_angle_d0.85075533
X-RAY DIFFRACTIONf_chiral_restr0.0557588
X-RAY DIFFRACTIONf_plane_restr0.0052715
X-RAY DIFFRACTIONf_dihedral_angle_d4.84932425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.940.23051330.1892828X-RAY DIFFRACTION93.79
1.94-1.990.22191420.17513029X-RAY DIFFRACTION99.81
1.99-2.050.21831440.1643028X-RAY DIFFRACTION99.97
2.05-2.120.23211430.16323029X-RAY DIFFRACTION100
2.12-2.190.21981440.15793058X-RAY DIFFRACTION100
2.19-2.280.20311430.15033045X-RAY DIFFRACTION100
2.28-2.390.19091430.1523035X-RAY DIFFRACTION100
2.39-2.510.20471450.15563078X-RAY DIFFRACTION99.97
2.51-2.670.17621430.15193035X-RAY DIFFRACTION99.97
2.67-2.880.20451460.15623078X-RAY DIFFRACTION99.97
2.88-3.160.19361440.15443075X-RAY DIFFRACTION99.97
3.16-3.620.17271450.14473079X-RAY DIFFRACTION99.69
3.62-4.560.17681420.13343026X-RAY DIFFRACTION96.97
4.56-25.210.17181430.16683020X-RAY DIFFRACTION93.58
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)
11.88601920277-0.724139994780.535056053911.94167223765-0.7737039207752.02743686428-0.0321857050217-0.08617841241780.1861103441240.0733565704276-0.0109800513219-0.112373751307-0.1363833891360.1426250897930.04407462601920.0835517777979-0.01305570389430.02105535673190.100549025562-0.03268165970360.0788814596401-1.2472282880334.282267025842.6954575562
21.14683573071-0.460635319387-0.1638309270671.225783249810.3958176936681.60279061797-0.0456691051667-0.141486798296-0.1354292000210.07506830496080.0440463988998-0.1717709512280.1740930900760.188540163822-0.03024693544740.1333244894510.007044634822570.009322694701120.1247628915720.01406141686790.1294393436874.1923428582817.762321544543.9042132249
30.482375223355-0.151134724551-0.5046254510330.3598618846080.4762410659281.302666279930.01676341858670.00318385416229-0.00568587747672-0.005920094765480.01541952768220.0198581104368-0.02853712114460.023916750828-0.01891798525930.127297803247-0.00668925508638-0.0008650286766620.09451667933410.006329925895220.1196870236823.7030637533914.49714600318.5352362912
41.783894138350.5967511596110.4084868217220.84648987410.2210046732630.7961377205890.0125804093539-0.06366771107730.1498099038030.08386589737370.0155507727274-0.107957856952-0.1199959389770.108273503429-0.03089739167950.123583470432-0.01042540485940.00295784544650.0942760042046-0.03530051109290.1356752970517.980580971418.031038390720.1571802957
50.269085854631-0.00812423080421-0.1724733845070.1773841627340.02631533182672.037156340380.03081963053660.05661244495170.0866195029123-0.02952270456010.0098779256641-0.0545514617489-0.2551964191140.0119393016376-0.03188865694210.139440117946-0.007146095575840.01078414402340.112883414760.004788655158330.1462063174694.4670360147522.31055631716.37189864714
61.033071207140.537874072245-0.2935823857061.41973155638-0.0345726977331.7218100133-0.003589952248740.0261456341410.0977115727156-0.04223434180440.0484810892192-0.137739854301-0.1652892111890.233268647973-0.03095646548360.0964552274483-0.007178684533480.0205396089590.132883799928-0.04243753775440.18239921849722.432898043517.223858480715.1578972764
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 126 )
2X-RAY DIFFRACTION2chain 'A' and (resid 127 through 188 )
3X-RAY DIFFRACTION3chain 'A' and (resid 189 through 238 )
4X-RAY DIFFRACTION4chain 'A' and (resid 239 through 373 )
5X-RAY DIFFRACTION5chain 'A' and (resid 374 through 454 )
6X-RAY DIFFRACTION6chain 'A' and (resid 455 through 513 )

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