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- PDB-5jy6: Structures of Streptococcus agalactiae GBS GAPDH in different enz... -

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Basic information

Entry
Database: PDB / ID: 5jy6
TitleStructures of Streptococcus agalactiae GBS GAPDH in different enzymatic states
ComponentsGlyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold / NAD / GAPDH / Glycolysis
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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)155,61012
Polymers152,8594
Non-polymers2,7518
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20210 Å2
ΔGint-139 kcal/mol
Surface area43780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.578, 107.465, 89.273
Angle α, β, γ (deg.)90.00, 104.07, 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: 0 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEAA2 - 33422 - 354
21ILEILEBB2 - 33422 - 354
12ALAALAAA3 - 33523 - 355
22ALAALACC3 - 33523 - 355
13ILEILEAA3 - 33423 - 354
23ILEILEDD3 - 33423 - 354
14ALAALABB3 - 33523 - 355
24ALAALACC3 - 33523 - 355
15ILEILEBB3 - 33423 - 354
25ILEILEDD3 - 33423 - 354
16ALAALACC3 - 33523 - 355
26ALAALADD3 - 33523 - 355

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 38214.867 Da / Num. of mol.: 4
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 / Cell line (production host): Rosetta(DE3)pLysS / Production host: Escherichia coli (E. coli)
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 / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.06 Å3/Da / Density % sol: 40.21 %
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: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2014 / Details: Mirrors
RadiationMonochromator: cryo cooled double crystal Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→86.6 Å / Num. obs: 82890 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 24.5 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 1.9 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSMarch 30, 2013data reduction
Aimless0.1.27data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QX6_A

Resolution: 2→86.6 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.158 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.163 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21625 4145 5 %RANDOM
Rwork0.19488 ---
obs0.19597 78706 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.477 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20.01 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2→86.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10020 0 180 520 10720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01910362
X-RAY DIFFRACTIONr_bond_other_d0.0040.029854
X-RAY DIFFRACTIONr_angle_refined_deg1.361.9714094
X-RAY DIFFRACTIONr_angle_other_deg1.064322628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13351327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15625.311450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.739151689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3411552
X-RAY DIFFRACTIONr_chiral_restr0.0710.21649
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211891
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022287
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_it1.3632.8455323
X-RAY DIFFRACTIONr_mcbond_other1.3622.8455322
X-RAY DIFFRACTIONr_mcangle_it2.1954.266645
X-RAY DIFFRACTIONr_mcangle_other2.1954.2616646
X-RAY DIFFRACTIONr_scbond_it1.7513.0345039
X-RAY DIFFRACTIONr_scbond_other1.7513.0345040
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8364.4597450
X-RAY DIFFRACTIONr_long_range_B_refined4.40222.42411384
X-RAY DIFFRACTIONr_long_range_B_other4.32622.31711211
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)
11A407800.05
12B407800.05
21A403960.03
22C403960.03
31A407020.05
32D407020.05
41B399600.06
42C399600.06
51B406080.05
52D406080.05
61C402920.04
62D402920.04
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 294 -
Rwork0.298 5824 -
obs--98.71 %

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