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

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Basic information

Entry
Database: PDB / ID: 9iim
TitleStructure of the complex of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii with nicotinamide adenine dinucleotide at 2.74 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, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 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 at 2.74 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
C: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,28712
Polymers152,2504
Non-polymers3,0388
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20280 Å2
ΔGint-172 kcal/mol
Surface area46240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.262, 167.618, 151.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#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
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O
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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5 / Details: 0.2M AMSO4.6H2O, 0.1M HEPES sodium (pH 7.5)

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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: 2.74→45.96 Å / Num. obs: 49521 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.98 / Rmerge(I) obs: 0.42 / Rpim(I) all: 0.11 / Net I/σ(I): 8.3
Reflection shellResolution: 2.74→2.83 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.98 / Mean I/σ(I) obs: 2 / Num. unique obs: 4512 / CC1/2: 0.61 / Rpim(I) all: 0.56 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→45.96 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.913 / SU B: 12.694 / SU ML: 0.246 / Cross valid method: FREE R-VALUE / ESU R: 0.983 / ESU R Free: 0.308
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2285 1536 3.104 %
Rwork0.1642 47953 -
all0.166 --
obs-49489 99.927 %
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: 40.316 Å2
Baniso -1Baniso -2Baniso -3
1-1.591 Å20 Å2-0 Å2
2---1.013 Å2-0 Å2
3----0.577 Å2
Refinement stepCycle: LAST / Resolution: 2.74→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10716 0 196 445 11357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01211164
X-RAY DIFFRACTIONr_bond_other_d0.0010.01610574
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.79615214
X-RAY DIFFRACTIONr_angle_other_deg0.4871.76124262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72851364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.683574
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.21354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.691101858
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.45810506
X-RAY DIFFRACTIONr_chiral_restr0.0650.21790
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213034
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022538
X-RAY DIFFRACTIONr_nbd_refined0.1960.21994
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2150.29865
X-RAY DIFFRACTIONr_nbtor_refined0.1750.25324
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.25828
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2431
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0930.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2170.26
X-RAY DIFFRACTIONr_nbd_other0.3020.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0710.22
X-RAY DIFFRACTIONr_mcbond_it2.8733.9215462
X-RAY DIFFRACTIONr_mcbond_other2.8653.9215462
X-RAY DIFFRACTIONr_mcangle_it4.6177.0376824
X-RAY DIFFRACTIONr_mcangle_other4.6197.0386825
X-RAY DIFFRACTIONr_scbond_it3.964.4945702
X-RAY DIFFRACTIONr_scbond_other3.9594.4925699
X-RAY DIFFRACTIONr_scangle_it6.4828.0088390
X-RAY DIFFRACTIONr_scangle_other6.4818.0048385
X-RAY DIFFRACTIONr_lrange_it8.69136.611875
X-RAY DIFFRACTIONr_lrange_other8.67836.54511834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-2.8110.341120.2873518X-RAY DIFFRACTION100
2.811-2.8880.3091020.2593406X-RAY DIFFRACTION100
2.888-2.9710.261100.243315X-RAY DIFFRACTION100
2.971-3.0620.2721050.2123215X-RAY DIFFRACTION100
3.062-3.1620.35900.2063143X-RAY DIFFRACTION99.9073
3.162-3.2720.267890.1793043X-RAY DIFFRACTION100
3.272-3.3950.215790.1822935X-RAY DIFFRACTION100
3.395-3.5330.234860.1752821X-RAY DIFFRACTION99.9312
3.533-3.6890.2061040.1862704X-RAY DIFFRACTION100
3.689-3.8680.215920.1542572X-RAY DIFFRACTION100
3.868-4.0760.234820.1442481X-RAY DIFFRACTION100
4.076-4.3210.171780.1112344X-RAY DIFFRACTION100
4.321-4.6160.207640.1082215X-RAY DIFFRACTION100
4.616-4.9820.159750.1122031X-RAY DIFFRACTION100
4.982-5.4510.191630.1291914X-RAY DIFFRACTION99.9494
5.451-6.0840.265570.1621739X-RAY DIFFRACTION99.9444
6.084-7.0050.235570.1541543X-RAY DIFFRACTION99.8752
7.005-8.530.269390.1471323X-RAY DIFFRACTION99.9266
8.53-11.860.147300.1091050X-RAY DIFFRACTION99.9075
11.86-45.960.237220.218641X-RAY DIFFRACTION98.5141

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