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- PDB-7pkc: Streptococcus pyogenes Apo-GapN C284S variant -

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Basic information

Entry
Database: PDB / ID: 7pkc
TitleStreptococcus pyogenes Apo-GapN C284S variant
ComponentsPutative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Apo-enzyme
Function / homology:
Function and homology information
Biological speciesStreptococcus pyogenes M49 591 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSchindelin, H. / Albert, L.
Funding support Germany, 1items
OrganizationGrant numberCountry
Not funded Germany
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 1.1May 1, 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
I: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
J: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
K: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
L: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
M: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
N: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
O: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
P: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)852,91572
Polymers847,63516
Non-polymers5,28056
Water114,5936361
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)213,04616
Polymers211,9094
Non-polymers1,13712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19020 Å2
ΔGint-203 kcal/mol
Surface area60320 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)213,41420
Polymers211,9094
Non-polymers1,50516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19850 Å2
ΔGint-202 kcal/mol
Surface area60290 Å2
MethodPISA
3
I: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
J: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
K: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
L: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,32219
Polymers211,9094
Non-polymers1,41315
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19270 Å2
ΔGint-200 kcal/mol
Surface area60910 Å2
MethodPISA
4
M: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
N: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
O: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
P: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,13417
Polymers211,9094
Non-polymers1,22513
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19190 Å2
ΔGint-188 kcal/mol
Surface area60790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.665, 126.036, 148.393
Angle α, β, γ (deg.)96.36, 104.81, 84.23
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 52977.188 Da / Num. of mol.: 16 / Mutation: C284S
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 6361 / 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: 2.03 Å3/Da / Density % sol: 39.31 % / Description: prism
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M lithium sulfate 0.1 M Bis-Tris pH 6.5 18 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Apr 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 1.499→47.634 Å / Num. obs: 744804 / % possible obs: 89.97 % / Observed criterion σ(F): 1.2 / Redundancy: 2.76 % / CC1/2: 0.9921 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.087 / Rrim(I) all: 0.151 / Net I/σ(I): 5.444
Reflection shellResolution: 1.499→1.635 Å / Redundancy: 2.89 % / Rmerge(I) obs: 0.705 / Mean I/σ(I) obs: 1.569 / Num. unique obs: 37234 / CC1/2: 0.4662 / Rpim(I) all: 0.497 / Rrim(I) all: 0.866 / % possible all: 63.75

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Processing

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

Resolution: 1.5→19.97 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.173 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.127 / SU Rfree Blow DPI: 0.117 / SU Rfree Cruickshank DPI: 0.116
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 18412 -RANDOM
Rwork0.1999 ---
obs0.2007 744550 68.6 %-
Displacement parametersBiso mean: 16.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.5078 Å2-4.5178 Å20.7058 Å2
2--3.0068 Å20.5407 Å2
3----2.499 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.5→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms56832 0 305 6361 63498
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.008118596HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.01215976HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d36233SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes18795HARMONIC5
X-RAY DIFFRACTIONt_it59260HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion8196SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies272HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact103794SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.74
X-RAY DIFFRACTIONt_other_torsion14.13
LS refinement shellResolution: 1.5→1.58 Å
RfactorNum. reflection% reflection
Rfree0.2842 359 -
Rwork0.2734 --
obs0.2737 14891 9.96 %
Refinement TLS params.Origin x: 24.4175 Å / Origin y: 37.514 Å / Origin z: -3.9711 Å
111213212223313233
T0.0064 Å2-0.0675 Å20.0124 Å2-0.0581 Å20.0067 Å2---0.0221 Å2
L-0.0038 °2-0.0061 °20.0046 °2-0.0008 °2-0 °2--0.003 °2
S-0.0016 Å °-0.0017 Å °0.0037 Å °-0.0017 Å °0.0024 Å °-0.0027 Å °0.0037 Å °-0.0027 Å °-0.0008 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }A2 - 475
2X-RAY DIFFRACTION1{ *|* }B2 - 475
3X-RAY DIFFRACTION1{ *|* }C1 - 475
4X-RAY DIFFRACTION1{ *|* }D0 - 475
5X-RAY DIFFRACTION1{ *|* }E2 - 475
6X-RAY DIFFRACTION1{ *|* }F2 - 475
7X-RAY DIFFRACTION1{ *|* }G2 - 475
8X-RAY DIFFRACTION1{ *|* }H0 - 475
9X-RAY DIFFRACTION1{ *|* }I0 - 475
10X-RAY DIFFRACTION1{ *|* }J2 - 475
11X-RAY DIFFRACTION1{ *|* }K0 - 475
12X-RAY DIFFRACTION1{ *|* }L0 - 475
13X-RAY DIFFRACTION1{ *|* }M0 - 475
14X-RAY DIFFRACTION1{ *|* }N2 - 475
15X-RAY DIFFRACTION1{ *|* }O0 - 475
16X-RAY DIFFRACTION1{ *|* }P0 - 475
17X-RAY DIFFRACTION1{ *|* }Q1 - 31
18X-RAY DIFFRACTION1{ *|* }W1 - 6365
19X-RAY DIFFRACTION1{ *|* }X501 - 704

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