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- PDB-8oha: Crystal structure of Leptospira interrogans GAPDH -

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Basic information

Entry
Database: PDB / ID: 8oha
TitleCrystal structure of Leptospira interrogans GAPDH
Components(Glyceraldehyde-3-phosphate ...) x 2
KeywordsHYDROLASE / GAPDH / Leptospira interrogans / Immune evasion / Innate immunity / Complement system
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glucose metabolic process / NAD binding / NADP binding
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesLeptospira interrogans serovar Copenhageni str. Fiocruz L1-130 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsNavas-Yuste, S. / de la Paz, K. / Querol-Garcia, J. / Gomez-Quevedo, S. / Rodriguez de Cordoba, S. / Fernandez, F.J. / Vega, M.C.
Funding support Spain, 6items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesRTI2018-102242-B-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-104912RB-I00 Spain
Autonomous Community of MadridS2017/BMD-3673 Spain
Autonomous Community of MadridS2022/BMD-7278 Spain
Spanish National Research CouncilSGL2103020 Spain
Spanish Ministry of Science, Innovation, and UniversitiesSAF2016-81876-REDT Spain
CitationJournal: Front Immunol / Year: 2023
Title: The structure of Leptospira interrogans GAPDH sheds light into an immunoevasion factor that can target the anaphylatoxin C5a of innate immunity.
Authors: Navas-Yuste, S. / de la Paz, K. / Querol-Garcia, J. / Gomez-Quevedo, S. / Rodriguez de Cordoba, S. / Fernandez, F.J. / Vega, M.C.
History
DepositionMar 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
C: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
E: Glyceraldehyde-3-phosphate dehydrogenase
F: Glyceraldehyde-3-phosphate dehydrogenase
G: Glyceraldehyde-3-phosphate dehydrogenase
H: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,27960
Polymers294,8108
Non-polymers9,46952
Water6,774376
1
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
C: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,48644
Polymers147,4214
Non-polymers6,06540
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29100 Å2
ΔGint-162 kcal/mol
Surface area45130 Å2
MethodPISA
2
E: Glyceraldehyde-3-phosphate dehydrogenase
F: Glyceraldehyde-3-phosphate dehydrogenase
G: Glyceraldehyde-3-phosphate dehydrogenase
H: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,79416
Polymers147,3894
Non-polymers3,40412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21520 Å2
ΔGint-129 kcal/mol
Surface area46050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.804, 82.039, 123.182
Angle α, β, γ (deg.)94.02, 95.15, 112.52
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

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Glyceraldehyde-3-phosphate ... , 2 types, 8 molecules ABCDFGHE

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase


Mass: 36855.277 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: Cys152 in chains A, B, C, D, F, G, and H has spontaneously oxidized to 3-sulfinoalanine (CSD).
Source: (gene. exp.) Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 (bacteria)
Gene: gapA / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72QM3
#2: Protein Glyceraldehyde-3-phosphate dehydrogenase


Mass: 36823.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 (bacteria)
Gene: gapA / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72QM3

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Non-polymers , 5 types, 428 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.5 Å3/Da / Density % sol: 50.8 %
Description: Elongated prisms with a dimension of 150-300 micromters in their longest axis
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Bis-Tris buffer, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2019
RadiationMonochromator: CHANNEL-CUT SI(111) + KB FOCUSING MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.37→45.5 Å / Num. obs: 110035 / % possible obs: 94.75 % / Redundancy: 3.6 % / Biso Wilson estimate: 51.17 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1077 / Rpim(I) all: 0.06522 / Rrim(I) all: 0.1262 / Net I/σ(I): 8.1
Reflection shellResolution: 2.37→2.455 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.285 / Num. unique obs: 10363 / CC1/2: 0.429 / CC star: 0.775 / Rpim(I) all: 0.7653 / Rrim(I) all: 1.498 / % possible all: 89.71

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4903: ???)refinement
XDS20190315data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→45.5 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2008 1.83 %Random selection
Rwork0.1908 ---
obs0.1916 109874 94.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20527 0 619 376 21522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01121510
X-RAY DIFFRACTIONf_angle_d1.22529084
X-RAY DIFFRACTIONf_dihedral_angle_d16.7688188
X-RAY DIFFRACTIONf_chiral_restr0.0683379
X-RAY DIFFRACTIONf_plane_restr0.0093648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.430.34291310.31977117X-RAY DIFFRACTION87
2.43-2.50.34291530.2957851X-RAY DIFFRACTION96
2.5-2.570.32721370.27127779X-RAY DIFFRACTION96
2.57-2.650.29761510.25537733X-RAY DIFFRACTION96
2.65-2.750.30551430.24717680X-RAY DIFFRACTION95
2.75-2.860.30041510.23667819X-RAY DIFFRACTION96
2.86-2.990.27011490.22867795X-RAY DIFFRACTION96
2.99-3.140.26541480.19767808X-RAY DIFFRACTION96
3.14-3.340.21681410.18367690X-RAY DIFFRACTION94
3.34-3.60.20911460.17627792X-RAY DIFFRACTION96
3.6-3.960.21211350.17077771X-RAY DIFFRACTION96
3.96-4.530.20821410.14867604X-RAY DIFFRACTION93
4.53-5.710.19431400.16467813X-RAY DIFFRACTION96
5.71-45.50.22231420.18537614X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.36430.0186-0.97692.09960.30521.7505-0.23590.3352-0.5866-0.0187-0.04980.12890.4479-0.27710.24210.4779-0.11860.00970.4372-0.0270.529163.656728.210641.643
21.0002-0.4415-1.05590.75550.17181.6354-0.01320.0112-0.04660.0055-0.01750.17090.0672-0.2670.02990.2976-0.077-0.03070.43110.00170.425958.117550.115451.9368
31.6688-0.3307-0.73962.8320.87572.02180.2194-0.10490.2567-0.122-0.0045-0.241-0.41760.2283-0.23080.4962-0.08650.13220.3497-0.00730.519179.827486.553546.8353
41.1192-0.3049-0.41621.5852-0.06251.4860.12710.0340.1038-0.0796-0.03840.0783-0.2402-0.208-0.07440.3137-0.00140.00440.3610.02590.371560.953671.126244.9274
53.13820.14830.54611.7050.54882.5011-0.0608-0.3465-0.17110.32230.14060.208-0.10590.027-0.0490.37040.0399-0.00380.53850.01520.427888.61851.5469.2215
61.0120.51570.75741.3587-0.91153.05280.179-0.29850.34190.2157-0.02190.25070.0029-0.2226-0.22580.4404-0.06520.02070.5351-0.01120.493679.720449.898769.3675
72.9908-0.938-0.33022.00720.78733.4046-0.0631-0.70180.5870.2640.4723-0.6444-0.30260.6482-0.38760.5059-0.0057-0.04550.8081-0.18510.637695.597458.314175.7276
80.5027-0.26070.44231.7731.58812.42750.0573-0.68921.07230.03130.2721-0.6668-0.51880.8889-0.2770.4724-0.1454-0.05070.9664-0.25570.8158105.036659.802765.6586
90.7737-0.6483-0.67331.59890.0091.08990.0187-0.44490.16490.12230.1121-0.16390.09350.3079-0.12680.2840.0015-0.06710.6672-0.03110.5148107.640746.231552.283
102.2396-0.7142-1.99344.8825-2.90584.68910.0944-0.87030.87310.1332-0.151-0.9381-0.58980.86290.03550.4068-0.10580.05040.6003-0.07820.6291.058766.965146.5257
113.5004-2.07230.90651.8069-0.48960.4828-0.1275-0.31770.52540.52960.0291-0.4367-0.2920.4609-0.00640.4126-0.0848-0.07020.7060.01040.6278102.351555.459744.8096
121.904-1.7592-0.26092.43260.05140.63260.1870.26670.0637-0.3381-0.2256-0.2109-0.07740.15060.03410.3357-0.0073-0.03250.48170.00370.5493101.276447.689939.9221
133.464-0.642-0.44772.37190.33682.077-0.00940.093-0.4999-0.2454-0.0566-0.39830.1510.31740.02120.40.02540.00940.4179-0.01840.631399.569432.813344.8662
142.2087-0.5524-2.02441.28850.64843.0334-0.03450.2718-0.198-0.1341-0.0143-0.09890.078-0.13190.07920.34850.0218-0.03540.42870.00590.560296.67639.512741.3447
151.34090.1709-0.11931.62860.66832.795-0.0415-0.2176-0.05950.08280.0507-0.2236-0.03150.1440.0380.3661-0.0176-0.00450.5113-0.01640.466699.456644.081855.3368
162.7055-0.712-0.50221.18420.67832.12280.26040.1645-0.2064-0.359-0.14220.0317-0.0376-0.1091-0.10960.56570.0502-0.00650.37250.05940.457275.982754.004210.8725
170.9378-0.23170.0531.4212-0.10091.14060.12530.04280.1441-0.3041-0.0268-0.3454-0.10420.2738-0.10180.3453-0.03340.11010.3957-0.01040.45395.733955.44225.7216
181.82270.4648-0.10942.16371.61812.44160.0777-0.010.16620.0403-0.37330.4747-0.2921-0.85850.28170.55030.1974-0.04240.7856-0.01950.54230.661590.16398.5768
191.30080.04110.01021.64641.01922.0643-0.04480.1599-0.0275-0.0301-0.0380.0127-0.0085-0.52230.10870.3942-0.0480.00130.4920.01810.307544.174371.482489.4945
202.5372-0.8495-0.58391.89590.5762.2199-0.1641-0.14920.00250.14640.2334-0.41630.3810.4666-0.07020.59450.1403-0.05480.5611-0.04410.522485.594764.0816107.3818
211.9203-0.16150.12920.42560.35551.26390.03080.2433-0.2367-0.11760.0066-0.15670.58150.1904-0.0320.81010.13260.01730.4397-0.02480.493771.350751.678994.4601
220.67380.76050.21192.0995-0.06190.4239-0.07040.1924-0.1146-0.14660.1432-0.45820.19910.1563-0.05670.58820.00590.00970.4669-0.030.458864.637567.501690.2591
231.2797-0.2434-0.02860.83120.19212.4627-0.0826-0.0264-0.1390.14730.02660.06550.6647-0.1430.06620.6734-0.05260.03690.33720.0250.369157.774755.2051103.1376
242.38870.3367-0.4411.82760.23373.42360.0535-0.02180.1029-0.17250.1172-0.3489-0.41720.4914-0.16560.6044-0.09040.04650.4971-0.00720.520676.185195.749282.3169
250.941-0.0883-0.42281.4817-0.16981.9770.054-0.0480.26660.05860.0426-0.1512-0.71970.1635-0.08440.6521-0.0540.03020.3583-0.04610.499569.2333102.4799104.9172
262.2380.3601-0.21072.49440.52232.3681-0.1446-0.26490.02060.47030.15590.11750.2825-0.136-0.03090.58820.1274-0.02890.44760.03880.361749.699477.159133.619
270.7914-0.028-0.19070.8720.04191.90230.0065-0.22080.11750.08720.1215-0.227-0.23840.2938-0.09850.5410.0427-0.05010.4603-0.09060.485867.800891.0188124.1257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 151 )
2X-RAY DIFFRACTION2chain 'A' and (resid 153 through 334 )
3X-RAY DIFFRACTION3chain 'B' and (resid -1 through 153 )
4X-RAY DIFFRACTION4chain 'B' and (resid 154 through 334 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 45 )
6X-RAY DIFFRACTION6chain 'C' and (resid 46 through 68 )
7X-RAY DIFFRACTION7chain 'C' and (resid 69 through 94 )
8X-RAY DIFFRACTION8chain 'C' and (resid 95 through 128 )
9X-RAY DIFFRACTION9chain 'C' and (resid 129 through 180 )
10X-RAY DIFFRACTION10chain 'C' and (resid 181 through 199 )
11X-RAY DIFFRACTION11chain 'C' and (resid 200 through 227 )
12X-RAY DIFFRACTION12chain 'C' and (resid 228 through 254 )
13X-RAY DIFFRACTION13chain 'C' and (resid 255 through 282 )
14X-RAY DIFFRACTION14chain 'C' and (resid 283 through 306 )
15X-RAY DIFFRACTION15chain 'C' and (resid 307 through 334 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 153 )
17X-RAY DIFFRACTION17chain 'D' and (resid 154 through 333 )
18X-RAY DIFFRACTION18chain 'E' and (resid 1 through 151 )
19X-RAY DIFFRACTION19chain 'E' and (resid 152 through 334 )
20X-RAY DIFFRACTION20chain 'F' and (resid 0 through 101 )
21X-RAY DIFFRACTION21chain 'F' and (resid 102 through 180 )
22X-RAY DIFFRACTION22chain 'F' and (resid 181 through 227 )
23X-RAY DIFFRACTION23chain 'F' and (resid 228 through 334 )
24X-RAY DIFFRACTION24chain 'G' and (resid 1 through 153 )
25X-RAY DIFFRACTION25chain 'G' and (resid 154 through 334 )
26X-RAY DIFFRACTION26chain 'H' and (resid 0 through 153 )
27X-RAY DIFFRACTION27chain 'H' and (resid 154 through 333 )

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