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- PDB-6ok4: Crystal Structure of Glyceraldehyde-3-phosphate dehydrogenase (GA... -

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Basic information

Entry
Database: PDB / ID: 6ok4
TitleCrystal Structure of Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Chlamydia trachomatis with bound NAD
ComponentsGlyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Glyceraldehyde-3-phosphate dehydrogenase / NAD / strain D/UW-3/Cx / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytosol
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 / Dihydrodipicolinate Reductase; domain 2 ...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 / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Protein Sci. / Year: 2020
Title: Structures of glyceraldehyde 3-phosphate dehydrogenase in Neisseria gonorrhoeae and Chlamydia trachomatis.
Authors: Barrett, K.F. / Dranow, D.M. / Phan, I.Q. / Michaels, S.A. / Shaheen, S. / Navaluna, E.D. / Craig, J.K. / Tillery, L.M. / Choi, R. / Edwards, T.E. / Conrady, D.G. / Abendroth, J. / Horanyi, ...Authors: Barrett, K.F. / Dranow, D.M. / Phan, I.Q. / Michaels, S.A. / Shaheen, S. / Navaluna, E.D. / Craig, J.K. / Tillery, L.M. / Choi, R. / Edwards, T.E. / Conrady, D.G. / Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Van Voorhis, W.C. / Zhang, Z. / Barrett, L.K. / Subramanian, S. / Staker, B. / Fan, E. / Myler, P.J. / Soge, O.O. / Hybiske, K. / Ojo, K.K.
History
DepositionApr 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: 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)154,06934
Polymers149,4554
Non-polymers4,61430
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23830 Å2
ΔGint-140 kcal/mol
Surface area43700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.470, 135.290, 137.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 0 and (name N or name...
21(chain B and (resid 0 through 16 or resid 18...
31(chain C and (resid 0 through 16 or resid 18...
41(chain D and ((resid 0 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 0 and (name N or name...A0
121(chain A and ((resid 0 and (name N or name...A-1 - 801
131(chain A and ((resid 0 and (name N or name...A-1 - 801
141(chain A and ((resid 0 and (name N or name...A-1 - 801
151(chain A and ((resid 0 and (name N or name...A-1 - 801
211(chain B and (resid 0 through 16 or resid 18...B0 - 16
221(chain B and (resid 0 through 16 or resid 18...B18 - 51
231(chain B and (resid 0 through 16 or resid 18...B53 - 57
241(chain B and (resid 0 through 16 or resid 18...B59 - 102
251(chain B and (resid 0 through 16 or resid 18...B0 - 901
261(chain B and (resid 0 through 16 or resid 18...B0 - 901
271(chain B and (resid 0 through 16 or resid 18...B0 - 901
281(chain B and (resid 0 through 16 or resid 18...B0 - 901
291(chain B and (resid 0 through 16 or resid 18...B0 - 901
311(chain C and (resid 0 through 16 or resid 18...C0 - 16
321(chain C and (resid 0 through 16 or resid 18...C18 - 26
331(chain C and (resid 0 through 16 or resid 18...C27
341(chain C and (resid 0 through 16 or resid 18...C-1 - 1601
351(chain C and (resid 0 through 16 or resid 18...C-1 - 1601
361(chain C and (resid 0 through 16 or resid 18...C-1 - 1601
371(chain C and (resid 0 through 16 or resid 18...C-1 - 1601
411(chain D and ((resid 0 and (name N or name...D0
421(chain D and ((resid 0 and (name N or name...D-1 - 701
431(chain D and ((resid 0 and (name N or name...D-1 - 701
441(chain D and ((resid 0 and (name N or name...D-1 - 701
451(chain D and ((resid 0 and (name N or name...D-1 - 701

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase / Glyceraldehyde 3-phosphate dehydrogenase / GAPDH / NAD-dependent glyceraldehyde-3-phosphate dehydrogenase


Mass: 37363.684 Da / Num. of mol.: 4 / Fragment: ChtrB.00839.a.B1 / Mutation: V71I, H72R, V105A, V292I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (strain D/UW-3/Cx) (bacteria)
Strain: D/UW-3/Cx / Gene: gap, gapA, CT_505 / Plasmid: ChtrB.00839.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0CE13, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

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Non-polymers , 6 types, 458 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: ChtrB.00839.a.B1.PW38497 (in 25 mM HEPES pH 7.0, 500 mM NaCl, 5% Glycerol , 2 mM DTT, and 0.025% Azide) at 17.29 mg/ml was incubated with 4 mM NAD and a small molecule (that is not in the ...Details: ChtrB.00839.a.B1.PW38497 (in 25 mM HEPES pH 7.0, 500 mM NaCl, 5% Glycerol , 2 mM DTT, and 0.025% Azide) at 17.29 mg/ml was incubated with 4 mM NAD and a small molecule (that is not in the electron density), then was mixed 1:1 with MCSG1(b9): 20% (w/v) PEG-3350, 0.2 M MgCl2, cryo: 20% ethylene glycol. Tray: 307039b9, puck: unc3-9.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 28, 2019 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→49.688 Å / Num. obs: 63802 / % possible obs: 99.9 % / Redundancy: 6.24 % / Biso Wilson estimate: 37.013 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.135 / Χ2: 1.019 / Net I/σ(I): 11.62 / Num. measured all: 398110 / Scaling rejects: 20
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.466.3090.6143.0629419466446630.8570.671100
2.46-2.536.3150.5063.6728542452045200.9130.553100
2.53-2.66.3030.4164.4128029444744470.9390.454100
2.6-2.686.3180.3784.8727062428542830.9420.413100
2.68-2.776.3120.3195.5426396418341820.9720.349100
2.77-2.876.3040.2726.5425499404640450.970.297100
2.87-2.986.3070.237.5124641390739070.9810.251100
2.98-3.16.2920.1899.0323568374637460.9830.207100
3.1-3.246.2840.17210.122591359535950.9820.188100
3.24-3.396.2770.13412.2321706345934580.9890.146100
3.39-3.586.2580.10514.8520695330733070.9930.115100
3.58-3.796.2510.09316.8519541312831260.9940.10299.9
3.79-4.066.2170.0818.7418259293929370.9960.08799.9
4.06-4.386.1860.06721.817048275627560.9960.073100
4.38-4.86.1780.05824.4715685254025390.9970.064100
4.8-5.376.1350.06223.1114122230423020.9970.06899.9
5.37-6.26.0910.06621.2212553206420610.9970.07399.9
6.2-7.595.9950.06223.2610473174717470.9960.068100
7.59-10.735.8470.04528.498122139013890.9980.04999.9
10.73-49.6885.2510.04328.3141598147920.9970.04897.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PYM

3pym


Resolution: 2.4→49.688 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.95
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 3566 5.99 %RANDOM
Rwork0.1721 ---
obs0.1743 59549 93.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.23 Å2 / Biso mean: 39.6749 Å2 / Biso min: 11.6 Å2
Refinement stepCycle: final / Resolution: 2.4→49.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9876 0 295 430 10601
Biso mean--50.45 37.01 -
Num. residues----1335
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5837X-RAY DIFFRACTION5.757TORSIONAL
12B5837X-RAY DIFFRACTION5.757TORSIONAL
13C5837X-RAY DIFFRACTION5.757TORSIONAL
14D5837X-RAY DIFFRACTION5.757TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3999-2.43280.32791260.26961973209983
2.4328-2.46750.30741470.25032028217585
2.4675-2.50440.26931310.24141993212486
2.5044-2.54350.27031190.23092121224088
2.5435-2.58520.27741360.22152058219488
2.5852-2.62980.25541290.20862102223188
2.6298-2.67760.21351390.20812100223989
2.6776-2.72910.28051330.20442097223089
2.7291-2.78480.25091290.19812186231591
2.7848-2.84530.26381190.19082171229091
2.8453-2.91150.23531510.18432201235293
2.9115-2.98430.21711590.19332231239094
2.9843-3.0650.2771470.18512254240194
3.065-3.15520.23011590.19252232239195
3.1552-3.2570.23391540.18142280243496
3.257-3.37340.22031400.17792316245697
3.3734-3.50840.1911250.1722355248097
3.5084-3.6680.20281500.15722348249898
3.668-3.86130.20261540.16252352250698
3.8613-4.10320.16181440.14772387253198
4.1032-4.41980.15141600.12152371253199
4.4198-4.86420.14991440.12482424256899
4.8642-5.56730.1771650.14362414257999
5.5673-7.0110.19531280.17362457258598
7.011-49.69840.18821780.16792532271098
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)
12.1762-0.2163-0.66731.20041.16792.9857-0.0190.3549-0.2081-0.0869-0.02150.02470.1531-0.06190.03950.2905-0.01380.00740.29280.01220.132-3.51421.6173-55.9874
21.9920.18640.02320.43390.07420.502-0.07770.12980.1114-0.03440.0009-0.1036-0.02260.10340.08770.20730.02140.02010.13860.02370.14489.231111.1596-37.2641
31.83020.094-0.08370.10620.28051.1096-0.016-1.09330.70330.24990.0620.0106-0.2570.24150.01240.47690.00850.00420.8768-0.25870.3835-5.87817.92942.2661
41.36910.09840.01360.4561-0.23830.5225-0.0394-0.58690.04350.0923-0.0175-0.10010.01090.01890.06080.23990.002-0.02790.3317-0.00990.14897.92557.7161-14.7419
51.85931.26120.14353.425-0.69351.6707-0.1537-0.2443-0.75830.2485-0.0471-0.16060.44620.16160.14850.35680.0440.08110.22240.09810.3771-14.6161-15.8552-18.8663
62.63060.94790.68644.85472.75365.86790.14290.3084-0.96320.093-0.2571-0.32930.7236-0.2569-0.04720.52530.11840.15140.36280.05980.8107-11.0683-25.1513-23.3124
72.5886-1.0365-0.29784.03240.21982.19510.04450.6556-1.1691-0.5668-0.10390.17340.42290.04010.05590.4915-0.0321-0.01260.3147-0.10820.628-30.8881-20.6519-27.6702
81.9605-0.0109-0.50090.2898-0.22740.7378-0.0525-0.1493-0.1652-0.00920.04760.03350.0697-0.1203-0.01830.2196-0.02110.00060.1590.00860.1412-33.58131.1066-22.3146
91.40280.11760.25672.48740.19920.23530.1019-0.28341.0720.2257-0.1137-0.1017-0.34320.0187-0.03380.4318-0.02960.00690.2592-0.07360.7599-15.449740.6061-31.4614
101.6563-0.0428-0.12510.3565-0.10430.8837-0.00030.16770.4569-0.03450.02910.0145-0.1327-0.1501-0.02660.2260.02640.00530.15560.02720.2536-32.745922.36-34.3391
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 149 )A-1 - 149
2X-RAY DIFFRACTION2chain 'A' and (resid 150 through 332 )A150 - 332
3X-RAY DIFFRACTION3chain 'B' and (resid 0 through 149 )B0 - 149
4X-RAY DIFFRACTION4chain 'B' and (resid 150 through 332 )B150 - 332
5X-RAY DIFFRACTION5chain 'C' and (resid -1 through 57 )C-1 - 57
6X-RAY DIFFRACTION6chain 'C' and (resid 58 through 84 )C58 - 84
7X-RAY DIFFRACTION7chain 'C' and (resid 85 through 149 )C85 - 149
8X-RAY DIFFRACTION8chain 'C' and (resid 150 through 332 )C150 - 332
9X-RAY DIFFRACTION9chain 'D' and (resid -1 through 128 )D-1 - 128
10X-RAY DIFFRACTION10chain 'D' and (resid 129 through 332 )D129 - 332

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