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- PDB-9krw: E. coli MaeB apo form -

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Basic information

Entry
Database: PDB / ID: 9krw
TitleE. coli MaeB apo form
ComponentsNADP-dependent malic enzyme
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: 3.85 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: Malic enzymes from different bacteria evolved distinct effector binding sites showing the same allosteric regulation mechanism
Authors: Sassa, M. / Yamato, H. / Tanino, H. / Fukuda, Y. / Inoue, T.
History
DepositionNov 28, 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
A: NADP-dependent malic enzyme
B: NADP-dependent malic enzyme
C: NADP-dependent malic enzyme
D: NADP-dependent malic enzyme
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
K: NADP-dependent malic enzyme
L: NADP-dependent malic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,000,08314
Polymers1,000,03412
Non-polymers492
Water00
1
A: NADP-dependent malic enzyme
B: NADP-dependent malic enzyme
C: NADP-dependent malic enzyme
D: NADP-dependent malic enzyme
E: NADP-dependent malic enzyme
F: NADP-dependent malic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)500,0417
Polymers500,0176
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: NADP-dependent malic enzyme
H: NADP-dependent malic enzyme
I: NADP-dependent malic enzyme
J: NADP-dependent malic enzyme
K: NADP-dependent malic enzyme
L: NADP-dependent malic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)500,0417
Polymers500,0176
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)347.708, 200.289, 201.823
Angle α, β, γ (deg.)90.000, 101.353, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 83336.164 Da / Num. of mol.: 12
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 3.44 Å3/Da / Density % sol: 64.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M Potassium chloride, 20% w/v PEG 3350

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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: Dec 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.85→49.47 Å / Num. obs: 127049 / % possible obs: 99.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 138.04 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.087 / Rrim(I) all: 0.165 / Net I/σ(I): 9.1
Reflection shellResolution: 3.85→3.92 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.315 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6295 / CC1/2: 0.537 / Rpim(I) all: 0.798 / Rrim(I) all: 1.541 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMACrefinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZNJ

6znj


Resolution: 3.85→49.47 Å / SU ML: 0.5221 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3957
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: The gap distance between residues ( F GLU 182 ) and ( F ASN 184 ) certainly seems large, but this was the limit due to the low resolution.
RfactorNum. reflection% reflection
Rfree0.24 6291 4.96 %
Rwork0.1954 120592 -
obs0.1976 126883 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 154.58 Å2
Refinement stepCycle: LAST / Resolution: 3.85→49.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms68717 0 2 0 68719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002769932
X-RAY DIFFRACTIONf_angle_d0.536594839
X-RAY DIFFRACTIONf_chiral_restr0.042511003
X-RAY DIFFRACTIONf_plane_restr0.005312462
X-RAY DIFFRACTIONf_dihedral_angle_d4.17799650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.85-3.890.37822050.363994X-RAY DIFFRACTION99.72
3.89-3.940.37372060.32974056X-RAY DIFFRACTION99.51
3.94-3.990.33582270.31184042X-RAY DIFFRACTION99.77
3.99-4.040.33371990.31344013X-RAY DIFFRACTION99.72
4.04-4.090.33091970.29914077X-RAY DIFFRACTION99.77
4.09-4.150.31922350.29413957X-RAY DIFFRACTION99.69
4.15-4.210.30822050.27354028X-RAY DIFFRACTION99.62
4.21-4.270.31292220.27094072X-RAY DIFFRACTION99.74
4.27-4.340.26661950.2584023X-RAY DIFFRACTION99.69
4.34-4.410.30582420.25573999X-RAY DIFFRACTION99.74
4.41-4.480.30981950.24264067X-RAY DIFFRACTION99.84
4.48-4.560.25862140.22984043X-RAY DIFFRACTION99.72
4.56-4.650.2772110.22134044X-RAY DIFFRACTION99.86
4.65-4.750.27071980.21994043X-RAY DIFFRACTION99.86
4.75-4.850.23082030.2094027X-RAY DIFFRACTION99.67
4.85-4.960.23292190.20474055X-RAY DIFFRACTION99.77
4.96-5.090.27072110.21864032X-RAY DIFFRACTION99.46
5.09-5.220.27181990.22114020X-RAY DIFFRACTION99.65
5.22-5.380.26992100.22794078X-RAY DIFFRACTION99.67
5.38-5.550.26362210.21584031X-RAY DIFFRACTION99.7
5.55-5.750.25012160.22424070X-RAY DIFFRACTION99.67
5.75-5.980.29992110.23664017X-RAY DIFFRACTION99.69
5.98-6.250.28092240.21194061X-RAY DIFFRACTION99.74
6.25-6.580.23722230.18824004X-RAY DIFFRACTION99.44
6.58-6.990.23222120.18724070X-RAY DIFFRACTION99.3
6.99-7.530.21571910.15824053X-RAY DIFFRACTION99.11
7.53-8.280.17942170.13284008X-RAY DIFFRACTION98.12
8.28-9.470.15792190.10873964X-RAY DIFFRACTION97.14
9.47-11.910.13281790.10113983X-RAY DIFFRACTION96.16
11.91-49.470.19461850.14513661X-RAY DIFFRACTION87.57

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