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- PDB-9h4x: Crystal structure of Ni2+ dependent glycerol-1-phosphate dehydrog... -

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Basic information

Entry
Database: PDB / ID: 9h4x
TitleCrystal structure of Ni2+ dependent glycerol-1-phosphate dehydrogenase AraM from Bacillus subtilis
ComponentsGlycerol-1-phosphate dehydrogenase [NAD(P)+]
KeywordsBIOSYNTHETIC PROTEIN / Lipid synthesis
Function / homology
Function and homology information


sn-glycerol-1-phosphate dehydrogenase / glycerol-1-phosphate dehydrogenase (NAD+) activity / glycerol-1-phosphate dehydrogenase (NADP+) activity / glycerophospholipid metabolic process / 3-dehydroquinate synthase activity / phospholipid biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Glycerol-1-phosphate dehydrogenase, bacteria / Glycerol-1-phosphate dehydrogenase / Iron-containing alcohol dehydrogenase / :
Similarity search - Domain/homology
1,3-DIHYDROXYACETONEPHOSPHATE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NICKEL (II) ION / Glycerol-1-phosphate dehydrogenase [NAD(P)+]
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsMao, T. / Pijning, T. / Guskov, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Ni2+ dependent glycerol-1-phosphate dehydrogenase AraM from Bacillus subtilis
Authors: Mao, T. / Pijning, T. / Guskov, A.
History
DepositionOct 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycerol-1-phosphate dehydrogenase [NAD(P)+]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1774
Polymers45,2821
Non-polymers8943
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Dynamic light scattering analysis, as well as size exclusion chromatography suggested the presence of dimers in solution. However, PISA analysis of the crystals did not find stable quaternary structures.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-21 kcal/mol
Surface area16350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.015, 70.499, 72.609
Angle α, β, γ (deg.)90, 95.51, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glycerol-1-phosphate dehydrogenase [NAD(P)+] / G1P dehydrogenase / G1PDH / Arabinose operon protein AraM / Enantiomeric glycerophosphate synthase ...G1P dehydrogenase / G1PDH / Arabinose operon protein AraM / Enantiomeric glycerophosphate synthase / sn-glycerol-1-phosphate dehydrogenase


Mass: 45282.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: egsA, araM, yseB, BSU28760 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P94527, sn-glycerol-1-phosphate dehydrogenase
#2: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE


Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.2 / Details: 20.0-25.5% (w/v) PEG 3350, 0.15-0.29 M KSCN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.95→45.51 Å / Num. obs: 9676 / % possible obs: 98.4 % / Redundancy: 1.9 % / CC1/2: 0.978 / Net I/σ(I): 8
Reflection shellResolution: 2.95→3.13 Å / Num. unique obs: 1527 / CC1/2: 0.433

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→43.036 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.837 / SU B: 66.295 / SU ML: 0.552 / Cross valid method: FREE R-VALUE / ESU R Free: 0.545
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3102 512 5.293 %
Rwork0.2406 9162 -
all0.245 --
obs-9674 98.114 %
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: 71.254 Å2
Baniso -1Baniso -2Baniso -3
1--1.805 Å2-0 Å2-0.435 Å2
2---0.747 Å2-0 Å2
3---2.588 Å2
Refinement stepCycle: LAST / Resolution: 2.95→43.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3027 0 55 11 3093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123139
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162997
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.824262
X-RAY DIFFRACTIONr_angle_other_deg0.5171.7616902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2675394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.316527
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.31252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94610531
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.49510135
X-RAY DIFFRACTIONr_chiral_restr0.0670.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023690
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02681
X-RAY DIFFRACTIONr_nbd_refined0.2110.2798
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.23095
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21498
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21763
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.262
X-RAY DIFFRACTIONr_metal_ion_refined0.030.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2230.219
X-RAY DIFFRACTIONr_nbd_other0.2550.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.25
X-RAY DIFFRACTIONr_mcbond_it3.163.9611579
X-RAY DIFFRACTIONr_mcbond_other3.163.9611579
X-RAY DIFFRACTIONr_mcangle_it5.0787.1371972
X-RAY DIFFRACTIONr_mcangle_other5.0777.1391973
X-RAY DIFFRACTIONr_scbond_it3.1854.2591560
X-RAY DIFFRACTIONr_scbond_other3.1844.261561
X-RAY DIFFRACTIONr_scangle_it5.217.7152290
X-RAY DIFFRACTIONr_scangle_other5.2097.7162291
X-RAY DIFFRACTIONr_lrange_it8.93148.85713475
X-RAY DIFFRACTIONr_lrange_other8.93248.85713476
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
2.95-3.0270.531250.3596910.3647260.8440.92598.62260.364
3.027-3.1090.277450.3486180.3436860.9430.92896.64720.35
3.109-3.1990.388300.3186320.3216890.8930.93796.08130.307
3.199-3.2970.336390.285850.2846690.9350.94393.27350.268
3.297-3.4040.267310.245600.2426390.9470.96692.48830.225
3.404-3.5230.331330.2445670.2496190.9290.96696.93050.226
3.523-3.6550.312260.2345800.2376060.9480.9661000.222
3.655-3.8030.363260.2385490.2455750.9330.9681000.217
3.803-3.970.214350.2085120.2095470.9750.9761000.195
3.97-4.1620.286240.1895270.1935510.9550.9791000.176
4.162-4.3850.279270.1924760.1965040.9570.97799.80160.181
4.385-4.6480.266280.1824450.1874730.9490.9781000.168
4.648-4.9650.296240.1974350.2034600.9550.97799.78260.185
4.965-5.3570.193250.214030.2084280.9710.9751000.201
5.357-5.8590.315200.2263720.233930.9370.97199.74550.213
5.859-6.5360.407170.2563340.2633520.920.96199.71590.246
6.536-7.5180.4210.2532930.2633160.9250.95399.36710.258
7.518-9.1380.23790.2472610.2462720.9720.95399.26470.256
9.138-12.6420.326170.2652000.272170.9190.9521000.275
12.642-43.0360.486100.3951230.4021350.9010.88798.51850.407
Refinement TLS params.Method: refined / Origin x: 20.4076 Å / Origin y: -10.5494 Å / Origin z: 16.1557 Å
111213212223313233
T0.0746 Å2-0.0232 Å20.0193 Å2-0.0458 Å2-0.0126 Å2--0.4706 Å2
L2.1629 °21.0047 °2-0.0206 °2-3.9845 °2-0.0084 °2--1.3522 °2
S0.1289 Å °-0.3099 Å °-0.0347 Å °0.4859 Å °-0.1561 Å °-0.068 Å °0.1156 Å °-0.006 Å °0.0272 Å °
Refinement TLS groupSelection: ALL

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