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- PDB-7pkj: Streptococcus pyogenes apo GapN -

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Basic information

Entry
Database: PDB / ID: 7pkj
TitleStreptococcus pyogenes apo GapN
ComponentsPutative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Apo-enzyme
Function / homologyBETA-MERCAPTOETHANOL / :
Function and homology information
Biological speciesStreptococcus pyogenes M49 591 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.989 Å
AuthorsSchindelin, H. / Albert, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Front Microbiol / Year: 2022
Title: The Non-phosphorylating Glyceraldehyde-3-Phosphate Dehydrogenase GapN Is a Potential New Drug Target in Streptococcus pyogenes.
Authors: Eisenberg, P. / Albert, L. / Teuffel, J. / Zitzow, E. / Michaelis, C. / Jarick, J. / Sehlke, C. / Grosse, L. / Bader, N. / Nunes-Alves, A. / Kreikemeyer, B. / Schindelin, H. / Wade, R.C. / Fiedler, T.
History
DepositionAug 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
B: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
C: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
D: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
E: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
F: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
G: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
H: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)428,60359
Polymers423,9468
Non-polymers4,65751
Water40,4082243
1
A: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
B: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
C: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
D: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,44731
Polymers211,9734
Non-polymers2,47427
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22340 Å2
ΔGint-251 kcal/mol
Surface area59650 Å2
MethodPISA
2
E: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
F: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
G: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
H: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,15528
Polymers211,9734
Non-polymers2,18224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22070 Å2
ΔGint-219 kcal/mol
Surface area59770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.749, 99.893, 106.182
Angle α, β, γ (deg.)77.67, 75.19, 67.12
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase


Mass: 52993.250 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes M49 591 (bacteria)
Gene: gapN, KUN4944_10090, SPNIH35_06470 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7G1J7Q1
#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2243 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.12 Å3/Da / Density % sol: 42.02 % / Description: Plate
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Lithium sulfate 0.1 M Bis-Tris pH 5.5 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.918401 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918401 Å / Relative weight: 1
ReflectionResolution: 1.989→48.148 Å / Num. obs: 153369 / % possible obs: 87.49 % / Observed criterion σ(I): 1.2 / Redundancy: 2.91 % / Biso Wilson estimate: 22.25 Å2 / CC1/2: 0.8467 / Rmerge(I) obs: 0.304 / Rpim(I) all: 0.213 / Rrim(I) all: 0.373 / Net I/σ(I): 3.195
Reflection shellResolution: 1.989→2.17 Å / Redundancy: 3.23 % / Rmerge(I) obs: 1.002 / Num. unique obs: 7668 / CC1/2: 0.3963 / Rpim(I) all: 0.655 / Rrim(I) all: 1.201 / % possible all: 70.72

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EUH

1euh


Resolution: 1.989→20.03 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.899 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.48 / SU Rfree Blow DPI: 0.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 7387 -RANDOM
Rwork0.1923 ---
obs0.1942 153157 62.9 %-
Displacement parametersBiso mean: 24.99 Å2
Baniso -1Baniso -2Baniso -3
1--2.2365 Å2-1.0871 Å21.8202 Å2
2---0.7198 Å22.7898 Å2
3---2.9564 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.989→20.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28376 0 272 2243 30891
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00858396HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.01106104HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d17709SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes9142HARMONIC5
X-RAY DIFFRACTIONt_it29288HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion4019SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies45HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact47413SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.35
X-RAY DIFFRACTIONt_other_torsion14.77
LS refinement shellResolution: 1.99→2.08 Å
RfactorNum. reflection% reflection
Rfree0.3204 146 -
Rwork0.2916 --
obs0.293 3064 9.84 %
Refinement TLS params.

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)
10.1363-0.0779-0.18610.1562-0.10640.5149-0.0693-0.01550.0828-0.01550.03120.04340.08280.04340.0381-0.0568-0.01660.0183-0.04490.04090.047416.2934-50.612410.0981
20.4262-0.1186-0.01730.3268-0.08980.1535-0.0107-0.02620.0351-0.02620.0176-0.03520.0351-0.0352-0.0069-0.0638-0.03840.0241-0.03420.03630.0308-8.9614-42.849-14.2361
30.21610.0565-0.08510.1484-0.05110.10210.00870.0044-0.01760.0044-0.00760.0075-0.01760.0075-0.0011-0.0672-0.02490.0417-0.03830.02720.068432.2712-15.6503-15.5487
40.2296-0.0036-0.1133-0.03220.02660.1804-0.0135-0.01690.0297-0.01690.0053-0.01660.0297-0.01660.0083-0.0522-0.0130.0458-0.04460.02620.055131.4019-44.8357-36.6459
50.17770.1811-0.00820.192-0.18980.5197-0.0712-0.03690.0341-0.03690.02410.06310.03410.06310.0471-0.0774-0.02820.03990.00420.05220.0005-21.077212.4645-83.2159
60.56420.11710.38450.2621-0.0540.35710.0118-0.0190.0775-0.019-0.08530.1920.07750.1920.0735-0.12120.04630.08960.06830.10540.04774.1913-7.1821-66.7445
70.17280.01620.02560.0765-0.0580.16740.00350.0055-0.01770.0055-0.01760.0016-0.01770.00160.0141-0.0591-0.02150.0285-0.0250.02450.0484-37.25081.7489-40.8796
80.23080.08130.06350.23260.02770.09830.0148-0.01530.0182-0.0153-0.00570.0110.01820.011-0.0091-0.0644-0.00650.0371-0.02110.01750.0193-36.3203-28.6488-60.5352
90.1594-0.1171-0.0750.024-0.05630.05090.0245-0.0595-0.0184-0.0595-0.0177-0.0426-0.0184-0.0426-0.0068-0.1347-0.0237-0.0905-0.108-0.04120.0382-4.0738-22.1349-38.2371
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 475
2X-RAY DIFFRACTION1{ A|* }A601
3X-RAY DIFFRACTION2{ B|* }B2 - 475
4X-RAY DIFFRACTION2{ B|* }B601
5X-RAY DIFFRACTION3{ C|* }C1 - 475
6X-RAY DIFFRACTION3{ C|* }C601
7X-RAY DIFFRACTION4{ D|* }D1 - 475
8X-RAY DIFFRACTION4{ D|* }D601
9X-RAY DIFFRACTION5{ E|* }E1 - 475
10X-RAY DIFFRACTION5{ E|* }E601
11X-RAY DIFFRACTION6{ F|* }F2 - 475
12X-RAY DIFFRACTION6{ F|* }F601
13X-RAY DIFFRACTION7{ G|* }G1 - 475
14X-RAY DIFFRACTION7{ G|* }G601
15X-RAY DIFFRACTION8{ H|* }H1 - 475
16X-RAY DIFFRACTION8{ H|* }H601
17X-RAY DIFFRACTION9{ A|}A604 - 605
18X-RAY DIFFRACTION9{ B|}B605 - 606
19X-RAY DIFFRACTION9{ C|}C605 - 606
20X-RAY DIFFRACTION9{ D|}D605 - 610
21X-RAY DIFFRACTION9{ E|}E604 - 605
22X-RAY DIFFRACTION9{ F|}F603 - 604
23X-RAY DIFFRACTION9{ G|}G604 - 610
24X-RAY DIFFRACTION9{ H|}H604 - 605

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