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- PDB-8zn1: Structure of erythrose-4-phosphate dehydrogenase from Acinetobact... -

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Basic information

Entry
Database: PDB / ID: 8zn1
TitleStructure of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii at 3.00 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: 3 Å
AuthorsViswanathan, V. / Kumari, A. / Singh, A. / Kumar, A. / Sharma, P. / Chopra, S. / 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 erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii at 3.00 A resolution
Authors: Viswanathan, V. / Kumari, A. / Singh, A. / Kumar, A. / Sharma, P. / Chopra, S. / Sharma, S. / Raje, C.I. / Singh, T.P.
History
DepositionMay 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 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)155,67216
Polymers152,2504
Non-polymers3,42212
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20960 Å2
ΔGint-239 kcal/mol
Surface area45950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.646, 167.880, 152.269
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.: 8 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 3.1 Å3/Da / Density % sol: 60.31 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: A reservoir solution containing 0.2 M MgCl2.6H2O, 0.1 M HEPES sodium (pH 7.5), and 30% v/v PEG 400 was prepared.

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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: 3→49.536 Å / Num. obs: 38162 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.971 / Rmerge(I) obs: 0.73 / Rpim(I) all: 0.21 / Rrim(I) all: 0.79 / Net I/σ(I): 7.3
Reflection shellResolution: 3→3.13 Å / Redundancy: 14.4 % / Rmerge(I) obs: 2.86 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4573 / CC1/2: 0.69 / Rpim(I) all: 0.78 / Rrim(I) all: 2.98 / % 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
Starting model: 3CMC

3cmc


Resolution: 3→49.536 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.894 / SU B: 19.96 / SU ML: 0.336 / Cross valid method: FREE R-VALUE / ESU R Free: 0.4
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2419 754 1.978 %
Rwork0.1658 37362 -
all0.167 --
obs-38116 99.893 %
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: 48.146 Å2
Baniso -1Baniso -2Baniso -3
1--0.227 Å20 Å2-0 Å2
2---3.798 Å20 Å2
3---4.025 Å2
Refinement stepCycle: LAST / Resolution: 3→49.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10716 0 216 265 11197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01211156
X-RAY DIFFRACTIONr_bond_other_d0.0010.01610548
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.79515204
X-RAY DIFFRACTIONr_angle_other_deg0.5061.76124204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87151360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.761572
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.43554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.348101852
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.20610504
X-RAY DIFFRACTIONr_chiral_restr0.0650.21792
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022524
X-RAY DIFFRACTIONr_nbd_refined0.2090.22120
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.210171
X-RAY DIFFRACTIONr_nbtor_refined0.180.25355
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.25944
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0310.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1690.217
X-RAY DIFFRACTIONr_nbd_other0.3490.257
X-RAY DIFFRACTIONr_mcbond_it3.3794.6745452
X-RAY DIFFRACTIONr_mcbond_other3.3774.6745452
X-RAY DIFFRACTIONr_mcangle_it5.4058.3916808
X-RAY DIFFRACTIONr_mcangle_other5.4058.3936809
X-RAY DIFFRACTIONr_scbond_it4.2095.2465704
X-RAY DIFFRACTIONr_scbond_other4.25.2445697
X-RAY DIFFRACTIONr_scangle_it6.8589.3968396
X-RAY DIFFRACTIONr_scangle_other6.8459.3938385
X-RAY DIFFRACTIONr_lrange_it9.20143.49311825
X-RAY DIFFRACTIONr_lrange_other9.243.49711823
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
3-3.0780.355630.30426940.30527570.8950.9331000.291
3.078-3.1620.356550.27326510.27427060.9250.9461000.256
3.162-3.2530.307460.22825810.2326270.9380.9641000.209
3.253-3.3530.253540.19525170.19625710.9590.9741000.177
3.353-3.4620.228510.17424250.17624770.9640.9899.95960.156
3.462-3.5830.287420.19923660.224080.9450.9731000.178
3.583-3.7170.424370.26723070.26923580.840.9599.40630.24
3.717-3.8680.258380.19921950.222370.9520.97399.82120.177
3.868-4.0390.186420.16221000.16321480.9650.98299.72070.142
4.039-4.2350.214410.12720200.12920610.9740.9881000.11
4.235-4.4620.274410.11919350.12119770.9580.9999.94940.104
4.462-4.730.186370.11318120.11418500.9770.99199.94590.101
4.73-5.0540.16390.11417310.11517700.9840.9921000.104
5.054-5.4540.215320.11516060.11716380.9750.9921000.107
5.454-5.9670.262330.15114810.15415140.970.9871000.14
5.967-6.660.298330.13913620.14313950.9720.9891000.13
6.66-7.6670.155270.12511960.12512230.9840.991000.119
7.667-9.3340.199230.110420.10210650.980.9941000.101
9.334-12.9720.129130.1078220.1078350.9930.9941000.113
12.972-49.5360.19570.2425190.2425270.9780.95499.81020.231

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