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- PDB-7ocu: Mannitol-1-phosphate bound to the phosphatase domain of the bifun... -

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Basic information

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


oxidoreductase activity / hydrolase activity
Similarity search - Function
Mannitol dehydrogenase, C-terminal / Mannitol dehydrogenase C-terminal domain / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / 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
Similarity search - Domain/homology
D-Mannitol-1-phosphate / BETA-MERCAPTOETHANOL / HAD hydrolase, family IA, variant 3
Similarity search - Component
Biological speciesAcinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 27, 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: Mannitol-1-phosphate dehydrogenase/phosphatase MtlD
B: Mannitol-1-phosphate dehydrogenase/phosphatase MtlD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,98612
Polymers167,0102
Non-polymers97510
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 area10310 Å2
ΔGint-117 kcal/mol
Surface area56220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.439, 157.433, 219.824
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 Mannitol-1-phosphate dehydrogenase/phosphatase MtlD / HAD hydrolase / family IA / variant 3


Mass: 83505.234 Da / Num. of mol.: 2 / Mutation: N374A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (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, 85 molecules

#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Chemical ChemComp-44H / D-Mannitol-1-phosphate / 1-O-phosphono-D-mannitol


Mass: 262.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O9P
#8: Water ChemComp-HOH / water / 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: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M BIS-Tris propane pH6.5, 0.25M 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 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.7→48.49 Å / Num. obs: 47757 / % possible obs: 100 % / Redundancy: 13.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.032 / Rrim(I) all: 0.119 / Net I/σ(I): 16.4 / Num. measured all: 664860 / Scaling rejects: 238
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
2.7-2.7914.31.9146645946470.8310.521.9842.2100
10.46-48.4912.40.039112309060.9990.0110.0450.599.1

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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: 2.7→48.49 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU B: 38.37 / SU ML: 0.351 / SU R Cruickshank DPI: 2.4761 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.476 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 2380 5 %RANDOM
Rwork0.2268 ---
obs0.2287 45334 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: 202.99 Å2 / Biso mean: 88.16 Å2 / Biso min: 45.19 Å2
Baniso -1Baniso -2Baniso -3
1--2.57 Å2-0 Å20 Å2
2---4.34 Å2-0 Å2
3---6.91 Å2
Refinement stepCycle: final / Resolution: 2.7→48.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11018 0 54 75 11147
Biso mean--98.69 62.64 -
Num. residues----1366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.01311281
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710492
X-RAY DIFFRACTIONr_angle_refined_deg1.1361.63915227
X-RAY DIFFRACTIONr_angle_other_deg1.0191.57524390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.69751362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.39523.28628
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.664152076
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6581564
X-RAY DIFFRACTIONr_chiral_restr0.0290.21454
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212482
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022274
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 188 -
Rwork0.351 3326 -
all-3514 -
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)
11.99520.39160.57631.6699-0.03011.24720.0077-0.4372-0.1950.7171-0.18490.01580.1374-0.00240.17730.4433-0.03280.07840.12360.04670.110145.5388.71179.346
21.1059-0.19120.50071.5747-0.62162.2209-0.0933-0.33870.29530.7164-0.03850.167-0.3548-0.15570.13190.47110.00820.05780.1654-0.22610.386934.50242.54979.967
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 692
2X-RAY DIFFRACTION1A801
3X-RAY DIFFRACTION2B2 - 694
4X-RAY DIFFRACTION2B801 - 802

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