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- PDB-6x2e: Crystal Structure of Chlamydia trachomatis mixed (apo/holo) Glyce... -

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Basic information

Entry
Database: PDB / ID: 6x2e
TitleCrystal Structure of Chlamydia trachomatis mixed (apo/holo) Glyceraldehyde 3-phosphate dehydrogenase
ComponentsGlyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / GAPDH / NAD / Glycolysis / Chlamydia
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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSchormann, N. / Chattopadhyay, D.
CitationJournal: Protein Sci. / Year: 2020
Title: Chlamydia trachomatis glyceraldehyde 3-phosphate dehydrogenase: Enzyme kinetics, high-resolution crystal structure, and plasminogen binding.
Authors: Schormann, N. / Campos, J. / Motamed, R. / Hayden, K.L. / Gould, J.R. / Green, T.J. / Senkovich, O. / Banerjee, S. / Ulett, G.C. / Chattopadhyay, D.
History
DepositionMay 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 18, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)147,6657
Polymers145,6744
Non-polymers1,9903
Water13,799766
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18200 Å2
ΔGint-127 kcal/mol
Surface area44880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.222, 104.240, 85.990
Angle α, β, γ (deg.)90.000, 97.480, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 51 or resid 53...
21(chain B and (resid 1 through 51 or resid 53...
31(chain C and (resid 1 through 51 or resid 53...
41(chain D and (resid 1 through 51 or resid 53...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLYGLY(chain A and (resid 1 through 51 or resid 53...AA1 - 511 - 51
12PHEPHEGLYGLY(chain A and (resid 1 through 51 or resid 53...AA53 - 6753 - 67
13ARGARGGLNGLN(chain A and (resid 1 through 51 or resid 53...AA69 - 8069 - 80
14LYSLYSLYSLYS(chain A and (resid 1 through 51 or resid 53...AA8181
15METMETSERSER(chain A and (resid 1 through 51 or resid 53...AA1 - 3331 - 333
16METMETSERSER(chain A and (resid 1 through 51 or resid 53...AA1 - 3331 - 333
17METMETSERSER(chain A and (resid 1 through 51 or resid 53...AA1 - 3331 - 333
18METMETSERSER(chain A and (resid 1 through 51 or resid 53...AA1 - 3331 - 333
21METMETGLYGLY(chain B and (resid 1 through 51 or resid 53...BB1 - 511 - 51
22PHEPHEGLYGLY(chain B and (resid 1 through 51 or resid 53...BB53 - 6753 - 67
23METMETSERSER(chain B and (resid 1 through 51 or resid 53...BB1 - 3331 - 333
24ASPASPALAALA(chain B and (resid 1 through 51 or resid 53...BB78 - 20778 - 207
25THRTHRLEULEU(chain B and (resid 1 through 51 or resid 53...BB209 - 217209 - 217
26LEULEUSERSER(chain B and (resid 1 through 51 or resid 53...BB219 - 248219 - 248
27ALAALAGLUGLU(chain B and (resid 1 through 51 or resid 53...BB250 - 276250 - 276
28ALAALAASNASN(chain B and (resid 1 through 51 or resid 53...BB278 - 332278 - 332
31METMETGLYGLY(chain C and (resid 1 through 51 or resid 53...CC1 - 511 - 51
32PHEPHEGLYGLY(chain C and (resid 1 through 51 or resid 53...CC53 - 6753 - 67
33METMETSERSER(chain C and (resid 1 through 51 or resid 53...CC1 - 3331 - 333
34METMETSERSER(chain C and (resid 1 through 51 or resid 53...CC1 - 3331 - 333
35LYSLYSLYSLYS(chain C and (resid 1 through 51 or resid 53...CC8181
36METMETSERSER(chain C and (resid 1 through 51 or resid 53...CC1 - 3331 - 333
37METMETSERSER(chain C and (resid 1 through 51 or resid 53...CC1 - 3331 - 333
38METMETSERSER(chain C and (resid 1 through 51 or resid 53...CC1 - 3331 - 333
39METMETSERSER(chain C and (resid 1 through 51 or resid 53...CC1 - 3331 - 333
310METMETSERSER(chain C and (resid 1 through 51 or resid 53...CC1 - 3331 - 333
41METMETGLYGLY(chain D and (resid 1 through 51 or resid 53...DD1 - 511 - 51
42PHEPHEGLUGLU(chain D and (resid 1 through 51 or resid 53...DD53 - 7653 - 76
43ASPASPGLNGLN(chain D and (resid 1 through 51 or resid 53...DD78 - 8078 - 80
44METMETNADNAD(chain D and (resid 1 through 51 or resid 53...DD - G1 - 4001
45METMETNADNAD(chain D and (resid 1 through 51 or resid 53...DD - G1 - 4001
46METMETNADNAD(chain D and (resid 1 through 51 or resid 53...DD - G1 - 4001
47METMETNADNAD(chain D and (resid 1 through 51 or resid 53...DD - G1 - 4001
48METMETNADNAD(chain D and (resid 1 through 51 or resid 53...DD - G1 - 4001

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Components

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


Mass: 36418.605 Da / Num. of mol.: 4
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: pJ411 / Production host: Escherichia coli (E. coli)
References: UniProt: P0CE13, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 766 / 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: 2.03 Å3/Da / Density % sol: 39.45 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 2000 MME, 0.1 M Hepes, pH 7.5; prior to crystallization the protein (at 30 mg/ml) was incubated with 1 mM NAD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→85.26 Å / Num. obs: 104308 / % possible obs: 97.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 17.1 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.059 / Rrim(I) all: 0.104 / Χ2: 1.03 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.832.80.6691.652730.640.470.822199.1
9.86-85.263.10.0316450.9980.020.03793.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18rc2_3794refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WYC

6wyc


Resolution: 1.8→85.26 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 5133 4.92 %
Rwork0.1749 99130 -
obs0.1771 104263 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.84 Å2 / Biso mean: 24.091 Å2 / Biso min: 6.35 Å2
Refinement stepCycle: final / Resolution: 1.8→85.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10142 0 132 766 11040
Biso mean--22.8 30.34 -
Num. residues----1328
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3804X-RAY DIFFRACTION6.325TORSIONAL
12B3804X-RAY DIFFRACTION6.325TORSIONAL
13C3804X-RAY DIFFRACTION6.325TORSIONAL
14D3804X-RAY DIFFRACTION6.325TORSIONAL
LS refinement shellResolution: 1.8→1.82 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3312 144 -
Rwork0.287 3373 -
obs--99 %

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