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- PDB-9ks0: E. coli MaeB PTA domain apo form -

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Basic information

Entry
Database: PDB / ID: 9ks0
TitleE. coli MaeB PTA domain apo form
Components(NADP-dependent malic enzyme) x 2
KeywordsSTRUCTURAL PROTEIN / oxidoreductase / cryo-EM / allostery
Function / homology
Function and homology information


malolactic enzyme activity / malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) / malate dehydrogenase (decarboxylating) (NADP+) activity / oxaloacetate decarboxylase activity / malate metabolic process / acyltransferase activity / NAD binding / manganese ion binding / identical protein binding / cytosol
Similarity search - Function
NAD(P)-dependent malic enzyme / Malic enzyme, NAD-binding domain, bacterial type / : / Phosphate acetyltransferase, domain 2 / Phosphate acetyltransferase, domain 1 / Phosphate acetyl/butaryl transferase / Phosphate acetyl/butaryl transferase / Malic enzyme, conserved site / Malic enzymes signature. / Malic enzyme, N-terminal domain ...NAD(P)-dependent malic enzyme / Malic enzyme, NAD-binding domain, bacterial type / : / Phosphate acetyltransferase, domain 2 / Phosphate acetyltransferase, domain 1 / Phosphate acetyl/butaryl transferase / Phosphate acetyl/butaryl transferase / Malic enzyme, conserved site / Malic enzymes signature. / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain / Malic enzyme, NAD binding domain / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP-dependent malic enzyme
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSassa, M. / Yamato, H. / Tanino, H. / Fukuda, Y. / Inoue, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: E. coli MaeB PTA domain apo form
Authors: Sassa, M. / Yamato, H. / Tanino, H. / Fukuda, Y. / Inoue, T.
History
DepositionNov 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: NADP-dependent malic enzyme
F: NADP-dependent malic enzyme
G: NADP-dependent malic enzyme
H: NADP-dependent malic enzyme
I: NADP-dependent malic enzyme
J: NADP-dependent malic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,9478
Polymers244,7556
Non-polymers1922
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.066, 130.026, 169.981
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
NADP-dependent malic enzyme / NADP-ME


Mass: 40789.793 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: maeB, ypfF, b2463, JW2447 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P76558, malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)
#2: Protein NADP-dependent malic enzyme / NADP-ME


Mass: 40805.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: maeB, ypfF, b2463, JW2447 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P76558, malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Ammonium sulfate, 0.05 M ADA, 13% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→47.88 Å / Num. obs: 59681 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 138.04 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.076 / Rrim(I) all: 0.196 / Net I/σ(I): 9.8
Reflection shellResolution: 2.8→2.88 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.297 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4598 / CC1/2: 0.788 / Rpim(I) all: 0.531 / Rrim(I) all: 1.403 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZN9

6zn9


Resolution: 2.8→47.876 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: FREE R-VALUE / ESU R Free: 0.387
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2592 2971 4.984 %
Rwork0.2142 56642 -
all0.216 --
obs-59613 99.915 %
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: 60.271 Å2
Baniso -1Baniso -2Baniso -3
1-0.007 Å2-0 Å2-0 Å2
2---0.018 Å20 Å2
3---0.011 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15407 0 10 163 15580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01315672
X-RAY DIFFRACTIONr_bond_other_d0.0340.01515386
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.64121223
X-RAY DIFFRACTIONr_angle_other_deg2.2751.57235337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.97751996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.05921.463820
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.771152765
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2515138
X-RAY DIFFRACTIONr_chiral_restr0.0450.22076
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217772
X-RAY DIFFRACTIONr_gen_planes_other0.0090.023481
X-RAY DIFFRACTIONr_nbd_refined0.1990.23131
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2280.214592
X-RAY DIFFRACTIONr_nbtor_refined0.1560.27596
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0650.27514
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2392
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.070.218
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3090.225
X-RAY DIFFRACTIONr_nbd_other0.40.268
X-RAY DIFFRACTIONr_mcbond_it2.0426.3018002
X-RAY DIFFRACTIONr_mcbond_other2.0426.3018001
X-RAY DIFFRACTIONr_mcangle_it3.4349.459992
X-RAY DIFFRACTIONr_mcangle_other3.4339.459993
X-RAY DIFFRACTIONr_scbond_it1.856.5997670
X-RAY DIFFRACTIONr_scbond_other1.8496.5957662
X-RAY DIFFRACTIONr_scangle_it3.239.79411231
X-RAY DIFFRACTIONr_scangle_other3.2299.78811219
X-RAY DIFFRACTIONr_lrange_it6.23574.89316634
X-RAY DIFFRACTIONr_lrange_other6.23574.89616634
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
2.8-2.8730.392130.34741200.34943350.6590.70699.95390.32
2.873-2.9510.3442230.33439970.33442200.6990.7381000.307
2.951-3.0360.3742150.30739200.3141390.7530.7999.90340.277
3.036-3.1290.3661870.30138060.30439950.7470.79999.94990.27
3.129-3.2310.3531900.29236920.29538850.80.83199.92280.26
3.231-3.3440.3131990.26935660.27137680.8420.85899.92040.24
3.344-3.470.2781970.24334420.24536430.880.89999.89020.217
3.47-3.6110.2821720.21933480.22235220.890.92299.94320.196
3.611-3.770.2411660.19531640.19733300.9210.9321000.178
3.77-3.9530.2361580.19430880.19632470.9260.93799.96920.176
3.953-4.1650.2571550.18929110.19230670.9150.93999.96740.174
4.165-4.4160.2221380.17127680.17329060.940.951000.158
4.416-4.7180.1861510.15526020.15627540.9550.9699.96370.145
4.718-5.0920.2471300.17224410.17525710.9310.9511000.161
5.092-5.5720.261020.20422730.20723750.9320.9351000.187
5.572-6.2190.335910.22920710.23321640.8650.91299.90760.209
6.219-7.1610.264850.19418490.19719370.9240.94399.84510.182
7.161-8.7210.182890.14815550.1516440.960.971000.147
8.721-12.1340.156680.14612620.14613300.9760.9791000.148
12.134-47.8760.233420.2777670.2748140.9410.92899.38570.285

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