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- PDB-9iil: Structure of the complex of erythrose-4-phosphate dehydrogenase f... -

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Basic information

Entry
Database: PDB / ID: 9iil
TitleStructure of the complex of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii with nicotinamide adenine dinucleotide in the presence of poly(ethylene glycol) at 2.20 A resolution
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / 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, 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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsViswanathan, V. / Kumari, A. / Singh, A. / Kumar, A. / Sharma, P. / Chopra, S. / Jeyakanthan, J. / Sharma, S. / Raje, C.I. / Singh, T.P.
Funding support India, 2items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB) India
Indian Council of Medical Research India
CitationJournal: To Be Published
Title: Structure of the complex of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii with nicotinamide adenine dinucleotide in the presence of poly(ethylene glycol) at 2.20 A resolution
Authors: Viswanathan, V. / Kumari, A. / Singh, A. / Kumar, A. / Sharma, P. / Chopra, S. / Jeyakanthan, J. / Sharma, S. / Raje, C.I. / Singh, T.P.
History
DepositionJun 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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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)158,95942
Polymers152,2504
Non-polymers6,70938
Water11,223623
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27030 Å2
ΔGint-41 kcal/mol
Surface area46720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.365, 167.131, 149.592
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase


Mass: 38062.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: epd, gap, A7M90_08740, Aba7835_13565, ABCAM1_1226, ABR2091_1144, APD17_19525, AYR68_05750, B7L45_13105, B9W25_17760, C2U32_02225, CAS83_00220, CBL15_12235, CTZ19_12640, D8O08_008145, DLI71_ ...Gene: epd, gap, A7M90_08740, Aba7835_13565, ABCAM1_1226, ABR2091_1144, APD17_19525, AYR68_05750, B7L45_13105, B9W25_17760, C2U32_02225, CAS83_00220, CBL15_12235, CTZ19_12640, D8O08_008145, DLI71_18430, EA706_09520, EA720_004470, EGM95_14355, F4T85_07645, FDN00_13975, FE003_13215, FJU42_18405, FJV09_11310, GSE42_06795, HBK86_03865, IAG11_16195, SAMEA4394745_03679
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A059ZTK9, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor

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Non-polymers , 10 types, 661 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#9: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: 0.2 M MgCl2.6H2O, 0.1M HEPES sodium (pH 7.5), 30% v/v PEG 400

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.2→88.454 Å / Num. obs: 91060 / % possible obs: 98.9 % / Redundancy: 13.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.064 / Rrim(I) all: 0.23 / Net I/σ(I): 9.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 14.4 % / Rmerge(I) obs: 2.38 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4425 / CC1/2: 0.725 / Rpim(I) all: 0.64 / Rrim(I) all: 2.46 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→88.454 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.152 / SU B: 6.775 / SU ML: 0.159 / Average fsc free: 0.9572 / Average fsc work: 0.9694 / Cross valid method: FREE R-VALUE / ESU R: 0.197 / ESU R Free: 0.175
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2167 1335 1.467 %
Rwork0.1683 89690 -
all0.169 --
obs-91025 98.692 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 45.029 Å2
Baniso -1Baniso -2Baniso -3
1--0.197 Å2-0 Å20 Å2
2--0.111 Å20 Å2
3---0.085 Å2
Refinement stepCycle: LAST / Resolution: 2.2→88.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10716 0 443 623 11782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01211402
X-RAY DIFFRACTIONr_bond_other_d0.0010.01610934
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.79615430
X-RAY DIFFRACTIONr_angle_other_deg0.5141.75425105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10851368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.111575
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.27954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59101863
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.17810507
X-RAY DIFFRACTIONr_chiral_restr0.0690.21793
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213073
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022547
X-RAY DIFFRACTIONr_nbd_refined0.2040.22156
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.210343
X-RAY DIFFRACTIONr_nbtor_refined0.1780.25414
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.26147
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2593
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0040.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2070.220
X-RAY DIFFRACTIONr_nbd_other0.2290.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.110.26
X-RAY DIFFRACTIONr_mcbond_it3.5254.3485474
X-RAY DIFFRACTIONr_mcbond_other3.5244.3485474
X-RAY DIFFRACTIONr_mcangle_it5.0877.7936840
X-RAY DIFFRACTIONr_mcangle_other5.0867.7956841
X-RAY DIFFRACTIONr_scbond_it4.7755.0645928
X-RAY DIFFRACTIONr_scbond_other4.7755.0645929
X-RAY DIFFRACTIONr_scangle_it7.3368.9848590
X-RAY DIFFRACTIONr_scangle_other7.3358.9848591
X-RAY DIFFRACTIONr_lrange_it9.37741.75412290
X-RAY DIFFRACTIONr_lrange_other9.38141.75112272
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.2-2.2570.332840.31265330.31267490.920.92498.04420.258
2.257-2.3190.2941070.28363480.28365780.9390.9498.13010.236
2.319-2.3860.321760.26262380.26364270.9290.94898.24180.221
2.386-2.4590.301870.24260470.24362280.9370.95798.49070.203
2.459-2.540.272990.22758290.22860330.9550.96398.25960.186
2.54-2.6290.277820.21556580.21658370.9520.96898.33820.181
2.629-2.7280.25720.19954920.19956420.9580.97498.61750.171
2.728-2.840.249820.19153180.19254690.9570.97698.73830.163
2.84-2.9660.242760.18550730.18652080.9630.97898.86710.161
2.966-3.110.258740.17248680.17350070.9540.98198.70180.153
3.11-3.2780.243670.16946340.1747470.9550.98299.0310.155
3.278-3.4770.202840.14644060.14745260.9790.98799.20460.137
3.477-3.7170.22650.14541470.14642450.9710.98799.22260.139
3.717-4.0140.151490.13638670.13639410.9860.98999.36560.133
4.014-4.3960.177470.12135950.12236690.9840.99199.26410.122
4.396-4.9130.141440.1132330.11133220.9880.99398.64540.112
4.913-5.670.138440.12628890.12629470.9890.99199.52490.129
5.67-6.9380.186460.14824730.14825280.9850.98899.6440.147
6.938-9.7810.18330.14219260.14219680.9850.98999.54270.149
9.781-88.4540.361170.22211160.22311590.9080.9797.75670.23

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