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- PDB-5jya: Structures of Streptococcus agalactiae GBS GAPDH in different enz... -

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Basic information

Entry
Database: PDB / ID: 5jya
TitleStructures of Streptococcus agalactiae GBS GAPDH in different enzymatic states
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold / NAD / GAPDH / Glycolysis / Ternary Complex
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / identical protein binding / metal ion binding / cytoplasm
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
GLYCERALDEHYDE-3-PHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsSchormann, N. / Chattopadhyay, D.
CitationJournal: PLoS ONE / Year: 2016
Title: Crystal Structures of Group B Streptococcus Glyceraldehyde-3-Phosphate Dehydrogenase: Apo-Form, Binary and Ternary Complexes.
Authors: Schormann, N. / Ayres, C.A. / Fry, A. / Green, T.J. / Banerjee, S. / Ulett, G.C. / Chattopadhyay, D.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)156,12912
Polymers152,7954
Non-polymers3,3348
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21870 Å2
ΔGint-126 kcal/mol
Surface area43830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.025, 108.681, 90.986
Angle α, β, γ (deg.)90.00, 105.81, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEAA3 - 33423 - 354
21ILEILEBB3 - 33423 - 354
12ALAALAAA3 - 33523 - 355
22ALAALACC3 - 33523 - 355
13ILEILEAA3 - 33423 - 354
23ILEILEDD3 - 33423 - 354
14ILEILEBB2 - 33422 - 354
24ILEILECC2 - 33422 - 354
15ALAALABB2 - 33522 - 355
25ALAALADD2 - 33522 - 355
16ILEILECC2 - 33422 - 354
26ILEILEDD2 - 33422 - 354

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase


Mass: 38198.801 Da / Num. of mol.: 4 / Mutation: C172S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria)
Gene: gap, gapA, EN72_09590, ERS039640_00200, ERS046921_00390, RDF_1710
Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: Q9ALW2, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
#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-G3H / GLYCERALDEHYDE-3-PHOSPHATE


Mass: 170.058 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7O6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.02 Å3/Da / Density % sol: 39.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20-28% PEG4000, 0.1M Mes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2015 / Details: Mirrors
RadiationMonochromator: Double-cooled crystal Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.85→87.55 Å / Num. obs: 29605 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 42.6 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.6
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.241 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QX6_A

Resolution: 2.85→87.55 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / SU B: 14.743 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.381 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21164 1969 6.7 %RANDOM
Rwork0.17419 ---
obs0.1767 27610 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.017 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å2-0.02 Å2
2--0.01 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.85→87.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10069 0 216 161 10446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01910456
X-RAY DIFFRACTIONr_bond_other_d0.0040.029917
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.97414218
X-RAY DIFFRACTIONr_angle_other_deg1.143322773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98751331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42525.264454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.113151695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7011553
X-RAY DIFFRACTIONr_chiral_restr0.0660.21662
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211951
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022304
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_it1.8384.2375348
X-RAY DIFFRACTIONr_mcbond_other1.8384.2375347
X-RAY DIFFRACTIONr_mcangle_it3.056.3466671
X-RAY DIFFRACTIONr_mcangle_other3.056.3466672
X-RAY DIFFRACTIONr_scbond_it1.984.3995108
X-RAY DIFFRACTIONr_scbond_other1.984.3985105
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3316.5097548
X-RAY DIFFRACTIONr_long_range_B_refined5.51332.35210773
X-RAY DIFFRACTIONr_long_range_B_other5.5132.35910770
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A389260.06
12B389260.06
21A389780.07
22C389780.07
31A385060.07
32D385060.07
41B392360.07
42C392360.07
51B393820.06
52D393820.06
61C390720.07
62D390720.07
LS refinement shellResolution: 2.847→2.921 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 129 -
Rwork0.26 1830 -
obs--89.66 %

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