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- PDB-7oct: NADPH bound to the dehydrogenase domain of the bifunctional manni... -

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Basic information

Entry
Database: PDB / ID: 7oct
TitleNADPH bound to the dehydrogenase domain of the bifunctional mannitol-1-phosphate dehydrogenase/phosphatase MtlD-N374A from Acinetobacter baumannii
ComponentsHAD hydrolase, family IA, variant 3
KeywordsOXIDOREDUCTASE / Mannitol / Dehydrogenase / Phosphatase / NADPH / Fructose-6-phosphate / HAD hydrolase family IA variant 3
Function / homology
Function and homology information


oxidoreductase activity / hydrolase activity / nucleotide binding / metal ion binding
Similarity search - Function
Mannitol dehydrogenase, C-terminal / Mannitol dehydrogenase C-terminal domain / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily ...Mannitol dehydrogenase, C-terminal / Mannitol dehydrogenase C-terminal domain / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / HAD superfamily / HAD-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / : / Chem-NDP / HAD hydrolase, family IA, variant 3
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsTam, H.K. / Mueller, V. / Pos, K.M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2251 Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Unidirectional mannitol synthesis of Acinetobacter baumannii MtlD is facilitated by the helix-loop-helix-mediated dimer formation.
Authors: Tam, H.K. / Konig, P. / Himpich, S. / Ngu, N.D. / Abele, R. / Muller, V. / Pos, K.M.
History
DepositionApr 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HAD hydrolase, family IA, variant 3
B: HAD hydrolase, family IA, variant 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,01722
Polymers167,0102
Non-polymers3,00720
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, Experiments were performed with the engineered disulfide-bonded crosslinked MtlD and supported by native gel electrophoresis and size exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15250 Å2
ΔGint-175 kcal/mol
Surface area54750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.304, 156.957, 220.028
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein HAD hydrolase, family IA, variant 3


Mass: 83505.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria)
Strain: ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81
Gene: HMPREF0010_00722 / Plasmid: PET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0C7J2

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Non-polymers , 9 types, 95 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#9: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.61 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M BIS-Tris propane pH6.5, 0.2M Na2SO4, 18% PEG3350, 0.02M MgCl2, 0.1M potassium acetate with microseeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.85→48.43 Å / Num. obs: 40545 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.051 / Rrim(I) all: 0.179 / Net I/σ(I): 13.1 / Num. measured all: 491072 / Scaling rejects: 114
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.85-2.9712.21.6525510345240.8330.4891.7242100
10.28-48.4311.40.043108419520.9990.0130.04538.799.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
REFMAC5.8.0258phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OCN

7ocn


Resolution: 2.85→48.43 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.896 / SU B: 43.46 / SU ML: 0.393 / SU R Cruickshank DPI: 0.3757 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2784 2054 5.1 %RANDOM
Rwork0.2273 ---
obs0.2298 38452 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 182.83 Å2 / Biso mean: 75.843 Å2 / Biso min: 18.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2---4.22 Å2-0 Å2
3---3.48 Å2
Refinement stepCycle: final / Resolution: 2.85→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11001 0 181 75 11257
Biso mean--76.26 42.92 -
Num. residues----1364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01311401
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710553
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.64715404
X-RAY DIFFRACTIONr_angle_other_deg1.0161.5824533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7851362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.66723.227629
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.953152075
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4581565
X-RAY DIFFRACTIONr_chiral_restr0.0290.21465
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212523
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022286
LS refinement shellResolution: 2.85→2.924 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 155 -
Rwork0.361 2805 -
all-2960 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8735-0.199-0.67221.4805-0.05251.3712-0.04090.39460.1012-0.635-0.10110.0284-0.0863-0.03040.1420.30340.0054-0.05820.104-0.00370.231-4.0599-8.840630.5843
20.98130.2136-0.4471.582-0.53511.9059-0.12960.2975-0.3007-0.65820.04620.12470.3947-0.13460.08340.3477-0.0473-0.04110.1329-0.22140.5471-14.9104-42.50229.8511
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 691
2X-RAY DIFFRACTION2B2 - 694

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