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

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Basic information

Entry
Database: PDB / ID: 7ocs
TitleMannitol-1-phosphate bound to the phosphatase domain of the bifunctional mannitol-1-phosphate dehydrogenase/phosphatase MtlD-D16A 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
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 / ACETATE ION / BETA-MERCAPTOETHANOL / TRIETHYLENE GLYCOL / 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: 2.3 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)338,58554
Polymers334,0174
Non-polymers4,56850
Water10,305572
1
A: HAD hydrolase, family IA, variant 3
D: HAD hydrolase, family IA, variant 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,54129
Polymers167,0092
Non-polymers2,53327
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13820 Å2
ΔGint-145 kcal/mol
Surface area55040 Å2
MethodPISA
2
B: HAD hydrolase, family IA, variant 3
C: HAD hydrolase, family IA, variant 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,04325
Polymers167,0092
Non-polymers2,03523
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12050 Å2
ΔGint-181 kcal/mol
Surface area51020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.888, 212.626, 98.819
Angle α, β, γ (deg.)90.000, 112.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 83504.250 Da / Num. of mol.: 4
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: PLASMID / Details (production host): pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0C7J2

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Non-polymers , 13 types, 622 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#7: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#10: Chemical
ChemComp-44H / D-Mannitol-1-phosphate / 1-O-phosphono-D-mannitol


Mass: 262.152 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15O9P
#11: 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
#12: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#13: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#14: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 53.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: .1M BIS-Tris propane pH6.5, 0.15M Na2SO4, 14% 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: 0.9788 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.3→48.61 Å / Num. obs: 149396 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 41.03 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.088 / Rrim(I) all: 0.237 / Net I/σ(I): 5.3 / Num. measured all: 1060197 / Scaling rejects: 661
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
2.3-2.347.11.8295251973910.6180.7331.9720.9100
12.6-48.616.50.05360359230.9980.0220.05814.698.5

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
BUSTERrefinement
PDB_EXTRACT3.27data extraction
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OCN

7ocn


Resolution: 2.3→48.61 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.863 / SU R Cruickshank DPI: 0.297 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.281 / SU Rfree Blow DPI: 0.211 / SU Rfree Cruickshank DPI: 0.218
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 7389 4.96 %RANDOM
Rwork0.2151 ---
obs0.2167 141672 99.8 %-
Displacement parametersBiso max: 135.44 Å2 / Biso mean: 53.47 Å2 / Biso min: 17.09 Å2
Baniso -1Baniso -2Baniso -3
1--24.2551 Å20 Å2-9.3863 Å2
2--6.3321 Å20 Å2
3---17.923 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: final / Resolution: 2.3→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21126 0 437 573 22136
Biso mean--61.96 42.62 -
Num. residues----2622
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d7914SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3685HARMONIC5
X-RAY DIFFRACTIONt_it21738HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2781SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact18005SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d21911HARMONIC1.30.008
X-RAY DIFFRACTIONt_angle_deg29660HARMONIC3.10.59
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion16.63
LS refinement shellResolution: 2.3→2.32 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2507 143 4.8 %
Rwork0.2329 2839 -
all0.2338 2982 -
obs--99.54 %
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)
10.1574-0.0393-0.09371.03380.05590.3764-0.01640.01730.01850.11740.03210.107-0.01650.0215-0.01570.01740.00820.0734-0.05560.0366-0.079-13.638318.32810.1084
20.4601-0.242-0.22740.29690.12240.92550.04890.0447-0.05310.0072-0.04860.03170.1492-0.0145-0.00030.09380.01990.0408-0.07710.0171-0.11410.3768-27.42116.2687
30.401-0.2938-0.13420.4117-0.0131.0424-0.0145-0.03850.13150.06-0.0199-0.09350.16550.15770.03440.0580.0809-0.0246-0.05130.0599-0.126228.73-28.762335.7128
40.1654-0.6419-0.16431.49940.08150.2-0.0247-0.07330.16490.13650.0249-0.4849-0.03460.048-0.0002-0.03-0.0661-0.0378-0.0591-0.0140.068118.412130.598114.4342
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|694 }A2 - 694
2X-RAY DIFFRACTION2{ B|2 - B|693 }B2 - 693
3X-RAY DIFFRACTION3{ C|2 - C|628 }C2 - 628
4X-RAY DIFFRACTION4{ D|2 - D|695 }D2 - 695

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