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- PDB-5j9g: Structure of Lactobacillus acidophilus glyceraldehyde-3-phosphate... -

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Basic information

Entry
Database: PDB / ID: 5j9g
TitleStructure of Lactobacillus acidophilus glyceraldehyde-3-phosphate dehydrogenase at 2.21 angstrom resolution
ComponentsGlyceraldehyde-3-p dehydrogenase
KeywordsOXIDOREDUCTASE / GAPDH / Lactobacillus acidophilus
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
Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsPatel, D. / Pappachan, A. / Singh, D.D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology India
CitationJournal: To Be Published
Title: Structure of Lactobacillus acidophilus glyceraldehyde-3-phosphate dehydrogenase at 2.21 angstrom resolution.
Authors: Patel, D. / Pappachan, A. / Singh, D.D.
History
DepositionApr 10, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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-p dehydrogenase
B: Glyceraldehyde-3-p dehydrogenase


Theoretical massNumber of molelcules
Total (without water)73,0692
Polymers73,0692
Non-polymers00
Water1,60389
1
A: Glyceraldehyde-3-p dehydrogenase
B: Glyceraldehyde-3-p dehydrogenase

A: Glyceraldehyde-3-p dehydrogenase
B: Glyceraldehyde-3-p dehydrogenase


Theoretical massNumber of molelcules
Total (without water)146,1384
Polymers146,1384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area14620 Å2
ΔGint-92 kcal/mol
Surface area45670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.990, 114.990, 113.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 1 - 338 / Label seq-ID: 1 - 338

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Glyceraldehyde-3-p dehydrogenase


Mass: 36534.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NDRI, Karnal, India
Source: (gene. exp.) Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM) (bacteria)
Strain: ATCC 700396 / NCK56 / N2 / NCFM / Gene: LBA0698 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta (DE3)
References: UniProt: Q5FL51, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.4 / Details: 10% w/v PEG 1000, 10% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 25, 2015 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.21→38.33 Å / Num. obs: 38437 / % possible obs: 99.9 % / Redundancy: 17.2 % / Biso Wilson estimate: 40.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Net I/av σ(I): 3.55 / Net I/σ(I): 16.5
Reflection shell% possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLM1.0.7data reduction
Aimless0.2.1data scaling
PHASER2.5.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QX6

4qx6


Resolution: 2.21→38.33 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.942 / SU B: 10.697 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.196 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 1708 4.6 %RANDOM
Rwork0.20325 ---
obs0.20427 35675 97.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 44.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å2-0 Å2
2---0.59 Å2-0 Å2
3---1.17 Å2
Refinement stepCycle: 1 / Resolution: 2.21→38.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5126 0 0 89 5215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195214
X-RAY DIFFRACTIONr_bond_other_d0.0040.025034
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.9577084
X-RAY DIFFRACTIONr_angle_other_deg1.2311588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7565674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.27924.906212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56915884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.081524
X-RAY DIFFRACTIONr_chiral_restr0.1010.2842
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215920
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021120
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_it0.8642.8852702
X-RAY DIFFRACTIONr_mcbond_other0.8652.8852701
X-RAY DIFFRACTIONr_mcangle_it1.4874.3243374
X-RAY DIFFRACTIONr_mcangle_other1.4874.3243375
X-RAY DIFFRACTIONr_scbond_it0.8772.9822512
X-RAY DIFFRACTIONr_scbond_other0.8772.9822513
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4494.4193711
X-RAY DIFFRACTIONr_long_range_B_refined2.82422.3835439
X-RAY DIFFRACTIONr_long_range_B_other2.79822.3525430
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 41688 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.214→2.271 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 143 -
Rwork0.234 2633 -
obs--99.53 %
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)
10.94430.1236-0.14491.19740.2050.96390.059-0.2061-0.02260.2165-0.01550.2375-0.0039-0.1813-0.04350.0687-0.03110.03730.12770.04280.09358.927.8514.734
21.5249-0.11630.07210.9384-0.02510.86990.03380.22450.2649-0.19040.00230.0099-0.2683-0.0065-0.03610.1967-0.04950.04970.08260.0160.080227.54151.198-10.808
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 338
2X-RAY DIFFRACTION2B1 - 338

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