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- PDB-7www: Crystal Structure of Moonlighting GAPDH protein of Lactobacillus ... -

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Basic information

Entry
Database: PDB / ID: 7www
TitleCrystal Structure of Moonlighting GAPDH protein of Lactobacillus gasseri
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE / NAD / Attenuates allergic asthma / Immunometabolism
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glucose metabolic process / NAD binding / NADP binding / cytoplasm
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesLactobacillus gasseri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsJeng, W.Y. / Chen, P.C. / Wang, J.Y.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)NSC 102-2311-B-006-006-MY3 Taiwan
Ministry of Science and Technology (MoST, Taiwan)107-2314-B-006 -046 -MY3 Taiwan
CitationJournal: To Be Published
Title: Moonlighting GAPDH protein of Lactobacillus gasseri attenuates allergic asthma via immunometabolism change in macrophages
Authors: Chen, P.C. / Hsieh, M.H. / Kuo, W.S. / Wu, L.S.H. / Kao, H.F. / Liu, L.F. / Liu, Z.G. / Jeng, W.Y. / Wang, J.Y.
History
DepositionFeb 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1383
Polymers37,4121
Non-polymers7252
Water4,450247
1
A: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,55112
Polymers149,6494
Non-polymers2,9028
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_547y+1/2,x-1/2,-z+5/21
crystal symmetry operation10_875-x+3,-y+2,z1
crystal symmetry operation16_777-y+5/2,-x+5/2,-z+5/21
Buried area20240 Å2
ΔGint-124 kcal/mol
Surface area43560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.922, 114.922, 118.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase


Mass: 37412.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus gasseri (bacteria)
Gene: gap, BXT97_01160, C3745_09540, F8244_01270, GTH50_07620
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1V3Y2M1
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M sodium cacodylate pH 6.5, 16% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2016
Details: VERTICALLY COLLIMATING PREMIRROR, TOROIDAL FOCUSING MIRROR
RadiationMonochromator: LN2-COOLED FIXED-EXIT DOUBLECRYSTAL SI(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.88→30 Å / Num. obs: 32168 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.02 / Rrim(I) all: 0.07 / Χ2: 1.325 / Net I/σ(I): 41.7
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 3031 / CC1/2: 0.96 / CC star: 0.99 / Rpim(I) all: 0.165 / Rrim(I) all: 0.572 / Χ2: 1.108 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LVF

3lvf


Resolution: 1.88→29.673 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.955 / SU B: 8.555 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.127
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1625 5.072 %RANDOM
Rwork0.1344 30413 --
all0.138 ---
obs-32038 98.469 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 44.881 Å2
Baniso -1Baniso -2Baniso -3
1--0.676 Å20 Å2-0 Å2
2---0.676 Å20 Å2
3---1.352 Å2
Refinement stepCycle: LAST / Resolution: 1.88→29.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 48 247 2829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122628
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.6613577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7625335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33223.217115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38315432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.221512
X-RAY DIFFRACTIONr_chiral_restr0.0990.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021933
X-RAY DIFFRACTIONr_nbd_refined0.2190.21249
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21836
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2191
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1540.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1910.228
X-RAY DIFFRACTIONr_mcbond_it5.3843.8251343
X-RAY DIFFRACTIONr_mcangle_it6.1645.721677
X-RAY DIFFRACTIONr_scbond_it7.1924.011285
X-RAY DIFFRACTIONr_scangle_it7.5395.8781900
X-RAY DIFFRACTIONr_lrange_it7.84553.5644041
X-RAY DIFFRACTIONr_rigid_bond_restr6.53832628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.9810.3132400.2034180X-RAY DIFFRACTION94.8701
1.981-2.1010.242400.1514056X-RAY DIFFRACTION97.019
2.101-2.2450.2451950.1383939X-RAY DIFFRACTION99.6385
2.245-2.4240.2371910.1233674X-RAY DIFFRACTION99.5108
2.424-2.6540.241790.1243400X-RAY DIFFRACTION99.5826
2.654-2.9640.2191690.1323094X-RAY DIFFRACTION99.5424
2.964-3.4170.2121540.1452721X-RAY DIFFRACTION99.6534
3.417-4.1710.1961260.1252351X-RAY DIFFRACTION99.438
4.171-5.8430.164780.1111872X-RAY DIFFRACTION99.6423
5.843-29.6730.217530.1541124X-RAY DIFFRACTION98.5762
Refinement TLS params.Method: refined / Origin x: 152.0421 Å / Origin y: 114.8557 Å / Origin z: 135.5388 Å
111213212223313233
T0.0041 Å2-0.0005 Å20 Å2-0.003 Å2-0.0008 Å2--0.1619 Å2
L0.0218 °20.0029 °20.0193 °2-0.0754 °2-0.002 °2--0.0175 °2
S0.0002 Å °-0.0045 Å °-0.0091 Å °-0.0158 Å °0.0075 Å °-0.0166 Å °0.0003 Å °-0.0048 Å °-0.0077 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA3 - 338
2X-RAY DIFFRACTION1ALLA401
3X-RAY DIFFRACTION1ALLA402
4X-RAY DIFFRACTION1ALLA501 - 747

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