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- PDB-7ocn: Crystal structure of the bifunctional mannitol-1-phosphate dehydr... -

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Basic information

Entry
Database: PDB / ID: 7ocn
TitleCrystal structure of the bifunctional mannitol-1-phosphate dehydrogenase/phosphatase MtlD 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
BROMIDE ION / HAD hydrolase, family IA, variant 3
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 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 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)168,13817
Polymers167,0972
Non-polymers1,04115
Water1,20767
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 area11030 Å2
ΔGint-151 kcal/mol
Surface area57060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.496, 157.418, 219.802
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-944-

HOH

21A-951-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 83548.258 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 , 7 types, 82 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.62 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M BIS-Tris propane pH6.5, 0.2M Na2SO4, 16% PEG3350, 0.02M MgCl2, 0.2M NaBr with microseeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→48.52 Å / Num. obs: 53387 / % possible obs: 100 % / Redundancy: 13.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.028 / Rrim(I) all: 0.103 / Net I/σ(I): 15.6 / Num. measured all: 741229 / Scaling rejects: 53
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
2.6-2.6814.21.9366504545870.7990.5282.0071.9100
10.72-48.5212.60.041107268520.9990.0120.04346.199.1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→48.52 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.938 / SU B: 36.534 / SU ML: 0.341 / SU R Cruickshank DPI: 0.8518 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.852 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2674 2615 4.9 %RANDOM
Rwork0.237 ---
obs0.2384 50729 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: 218.91 Å2 / Biso mean: 92.703 Å2 / Biso min: 42.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å20 Å2
2---4.45 Å20 Å2
3---4.52 Å2
Refinement stepCycle: final / Resolution: 2.6→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11053 0 51 67 11171
Biso mean--103.8 63.31 -
Num. residues----1369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.01311297
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710488
X-RAY DIFFRACTIONr_angle_refined_deg1.1381.63715243
X-RAY DIFFRACTIONr_angle_other_deg1.0211.57424383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.70251363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.69523.344634
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.847152081
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5271564
X-RAY DIFFRACTIONr_chiral_restr0.0290.21450
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212514
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022278
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 189 -
Rwork0.344 3713 -
all-3902 -
obs--99.97 %
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)
11.92480.12170.71561.4859-0.27641.8593-0.1203-0.3797-0.10080.6004-0.1551-0.0459-0.0818-0.07240.27540.3365-0.0038-0.04130.1014-0.00630.175645.67759.4358-30.3036
21.1851-0.24650.55911.4302-0.83451.7261-0.2877-0.27540.36390.71270.07750.0403-0.5913-0.25020.21020.70830.1706-0.15110.1906-0.25850.54534.807243.0114-29.8387
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 1301
2X-RAY DIFFRACTION2B2 - 901

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