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- PDB-6iqm: Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehy... -

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Basic information

Entry
Database: PDB / ID: 6iqm
TitleCrystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with NAD+ from Lactobacillus plantarum
ComponentsGlyceraldehyde-3-phosphate dehydrogenase, type I
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, 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, 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 ...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 domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesLactobacillus plantarum subsp. plantarum JCM 1149 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsYoneda, K. / Kinoshita, H.
CitationJournal: Milk Sci / Year: 2019
Title: Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase from Lactobacillus plantarum: Insight into the Mercury Binding Mechanism
Authors: Yoneda, K. / Ogata, M. / Nishiyama, K. / Fukuda, K. / Yasuda, S. / Igoshi, K. / Kinoshita, H.
History
DepositionNov 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase, type I
B: Glyceraldehyde-3-phosphate dehydrogenase, type I
C: Glyceraldehyde-3-phosphate dehydrogenase, type I
D: Glyceraldehyde-3-phosphate dehydrogenase, type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,99014
Polymers145,9044
Non-polymers3,08610
Water21,2761181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21220 Å2
ΔGint-75 kcal/mol
Surface area43570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.207, 171.953, 149.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-811-

HOH

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Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase, type I


Mass: 36475.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum subsp. plantarum JCM 1149 (bacteria)
Gene: gap, HMPREF0531_11006 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA2 PLYSS
References: UniProt: D7VA33, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-NAD / 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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1181 / 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: 2.53 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 25% (w/v) PEG 1500, 0.1M MIB buffer (pH 5.0)

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Feb 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→101.74 Å / Num. obs: 137453 / % possible obs: 99.1 % / Redundancy: 9.4 % / Biso Wilson estimate: 17.28 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 27.3
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.315 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J9G

5j9g


Resolution: 1.85→101.74 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.199 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19045 6891 5 %RANDOM
Rwork0.15851 ---
obs0.16012 130516 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.401 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.85→101.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10065 0 204 1181 11450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.01910447
X-RAY DIFFRACTIONr_bond_other_d0.0020.029653
X-RAY DIFFRACTIONr_angle_refined_deg2.1551.97614208
X-RAY DIFFRACTIONr_angle_other_deg1.192322362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.59451331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.66824.989435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.85151689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9421548
X-RAY DIFFRACTIONr_chiral_restr0.1760.21684
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211659
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022041
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3082.0195346
X-RAY DIFFRACTIONr_mcbond_other2.3042.0195344
X-RAY DIFFRACTIONr_mcangle_it3.1673.016669
X-RAY DIFFRACTIONr_mcangle_other3.1673.016670
X-RAY DIFFRACTIONr_scbond_it3.4152.3485101
X-RAY DIFFRACTIONr_scbond_other3.4152.3485101
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9463.397539
X-RAY DIFFRACTIONr_long_range_B_refined6.82226.0611986
X-RAY DIFFRACTIONr_long_range_B_other6.67125.58911714
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.847→1.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 478 -
Rwork0.17 9230 -
obs--95.37 %

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