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- PDB-6px2: Acropora millepora GAPDH -

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Basic information

Entry
Database: PDB / ID: 6px2
TitleAcropora millepora GAPDH
ComponentsGlyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / complex with NAD
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
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 / PHOSPHATE ION / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesAcropora millepora (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBrandt, G.S. / Fields, P.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS-1654249 United States
CitationJournal: Rsc Adv / Year: 2021
Title: Thermal stability and structure of glyceraldehyde-3-phosphate dehydrogenase from the coral Acropora millepora.
Authors: Perez, A.M. / Wolfe, J.A. / Schermerhorn, J.T. / Qian, Y. / Cela, B.A. / Kalinowski, C.R. / Largoza, G.E. / Fields, P.A. / Brandt, G.S.
History
DepositionJul 24, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionDec 25, 2019ID: 6DFZ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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
Revision 1.3Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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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)317,67624
Polymers311,6098
Non-polymers6,06716
Water4,017223
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)158,83812
Polymers155,8044
Non-polymers3,0348
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20610 Å2
ΔGint-153 kcal/mol
Surface area43410 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)158,83812
Polymers155,8044
Non-polymers3,0348
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20550 Å2
ΔGint-152 kcal/mol
Surface area43340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.219, 79.117, 138.819
Angle α, β, γ (deg.)76.680, 77.700, 67.980
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase / Glyceraldehyde 3-phosphate dehydrogenase


Mass: 38951.078 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acropora millepora (invertebrata) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A3F2YLZ0, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6 M SODIUM CITRATE, PH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2017
RadiationMonochromator: DOUBLE SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→19.95 Å / Num. obs: 183232 / % possible obs: 90.56 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.049 / Rrim(I) all: 0.07 / Net I/σ(I): 10
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.85 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 11180 / CC1/2: 0.911 / Rpim(I) all: 0.241 / Rrim(I) all: 0.341 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K9D

4k9d


Resolution: 2.4→19.95 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 28.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 9143 4.99 %
Rwork0.2091 173934 -
obs0.2103 183077 78.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.51 Å2 / Biso mean: 67.64 Å2 / Biso min: 24.53 Å2
Refinement stepCycle: final / Resolution: 2.4→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20255 0 392 223 20870
Biso mean--66.41 56.74 -
Num. residues----2656
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.42720.34283180.3264589781
2.4272-2.45570.34933170.3151598781
2.4557-2.48560.31212910.3036572179
2.4856-2.5170.34822930.3005600080
2.517-2.55010.3183220.2888580179
2.5501-2.58490.31183110.2791597081
2.5849-2.62180.28773150.2708596681
2.6218-2.66080.32643090.2736588480
2.6608-2.70230.30153070.2664583080
2.7023-2.74650.2682770.2668583279
2.7465-2.79380.29343310.2598579379
2.7938-2.84440.27842750.2502567377
2.8444-2.8990.27113110.2395570577
2.899-2.9580.27332820.2424541174
2.958-3.02210.27452730.2322517870
3.0221-3.09210.27262920.2305495269
3.0921-3.16910.25932660.2363559576
3.1691-3.25450.2453120.2249605081
3.2545-3.34980.2412830.2141594282
3.3498-3.45740.24993190.2208600782
3.4574-3.58030.26123270.2198596581
3.5803-3.72270.2683180.2172592381
3.7227-3.8910.23363300.2066589780
3.891-4.09450.22922900.1863565577
4.0945-4.34850.22143030.1806588179
4.3485-4.68030.17333160.1619583980
4.6803-5.14390.17313060.1768585179
5.1439-5.87160.18882880.1876524272
5.8716-7.33590.19843140.1938602782
7.3359-19.950.16833470.1632646088

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