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- PDB-1h5q: Mannitol dehydrogenase from Agaricus bisporus -

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Basic information

Entry
Database: PDB / ID: 1h5q
TitleMannitol dehydrogenase from Agaricus bisporus
ComponentsNADP-DEPENDENT MANNITOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / MANNITOL METABOLISM
Function / homology
Function and homology information


mannitol 2-dehydrogenase (NADP+) / mannitol 2-dehydrogenase (NADP+) activity / mannitol metabolic process / oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / NADP binding / protein homotetramerization
Similarity search - Function
Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NICKEL (II) ION / NADP-dependent mannitol dehydrogenase
Similarity search - Component
Biological speciesAGARICUS BISPORUS (common mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHorer, S. / Stoop, J. / Mooibroek, H. / Baumann, U. / Sassoon, J.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: The Crystallographic Structure of the Mannitol 2-Dehydrogenase Nadp+ Binary Complex from Agaricus Bisporus
Authors: Horer, S. / Stoop, J. / Mooibroek, H. / Baumann, U. / Sassoon, J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and Preliminary Crystallographic Analysis of Mannitol Dehydrogenase (Mtdh) from the Common Mushroom Agaricus Bisporus
Authors: Sassoon, J. / Horer, S. / Stoop, J. / Mooibroek, H. / Baumann, U.
History
DepositionMay 24, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADP-DEPENDENT MANNITOL DEHYDROGENASE
B: NADP-DEPENDENT MANNITOL DEHYDROGENASE
C: NADP-DEPENDENT MANNITOL DEHYDROGENASE
D: NADP-DEPENDENT MANNITOL DEHYDROGENASE
E: NADP-DEPENDENT MANNITOL DEHYDROGENASE
F: NADP-DEPENDENT MANNITOL DEHYDROGENASE
G: NADP-DEPENDENT MANNITOL DEHYDROGENASE
H: NADP-DEPENDENT MANNITOL DEHYDROGENASE
I: NADP-DEPENDENT MANNITOL DEHYDROGENASE
J: NADP-DEPENDENT MANNITOL DEHYDROGENASE
K: NADP-DEPENDENT MANNITOL DEHYDROGENASE
L: NADP-DEPENDENT MANNITOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,12830
Polymers338,85512
Non-polymers9,27318
Water57,4863191
1
A: NADP-DEPENDENT MANNITOL DEHYDROGENASE
B: NADP-DEPENDENT MANNITOL DEHYDROGENASE
C: NADP-DEPENDENT MANNITOL DEHYDROGENASE
D: NADP-DEPENDENT MANNITOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,04310
Polymers112,9524
Non-polymers3,0916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: NADP-DEPENDENT MANNITOL DEHYDROGENASE
F: NADP-DEPENDENT MANNITOL DEHYDROGENASE
G: NADP-DEPENDENT MANNITOL DEHYDROGENASE
H: NADP-DEPENDENT MANNITOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,04310
Polymers112,9524
Non-polymers3,0916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
I: NADP-DEPENDENT MANNITOL DEHYDROGENASE
J: NADP-DEPENDENT MANNITOL DEHYDROGENASE
K: NADP-DEPENDENT MANNITOL DEHYDROGENASE
L: NADP-DEPENDENT MANNITOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,04310
Polymers112,9524
Non-polymers3,0916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)227.250, 124.850, 132.690
Angle α, β, γ (deg.)90.00, 118.54, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.80324, 0.04937, 0.5936), (0.04647, -0.99872, 0.02019), (0.59384, 0.01137, -0.80451)-60.14751, 17.01104, 181.15178
2given(-0.91392, -0.33039, -0.2358), (-0.32648, 0.25315, 0.91068), (-0.24119, 0.90926, -0.33922)47.99002, -83.88606, 132.90018
3given(-0.89258, 0.28329, -0.35079), (0.28335, -0.25275, -0.92511), (-0.35073, -0.92513, 0.14533)53.69613, 105.51811, 101.60969
4given(0.99872, 0.04614, 0.02094), (-0.04887, 0.98632, 0.15742), (-0.01339, -0.15824, 0.98731)37.69871, -14.36648, -51.37036
5given(37.698711, -14.36648, -51.370361), (0.10102, -0.98519, -0.13854), (0.56673, 0.17144, -0.80587)-17.63614, 34.10699, 125.67982
6given(-0.9311, -0.30042, -0.20689), (-0.32226, 0.41174, 0.85242), (-0.1709, 0.86036, -0.48018)85.20172, -78.11904, 92.80707
7given(85.201721, -78.119041, 92.807068), (0.26545, -0.40771, -0.87367), (-0.38176, -0.87657, 0.29307)98.15092, 103.18123, 31.70274
8given(-0.869, -0.22454, -0.44092), (-0.26093, -0.54918, 0.79393), (-0.42042, 0.80497, 0.41865)45.85154, -63.66961, -15.39087
9given(-0.96993, 0.17071, -0.17348), (0.23957, 0.544, -0.80416), (-0.0429, -0.82154, -0.56854)15.22307, 86.40319, 99.03665
10given(0.97547, -0.15926, 0.15194), (0.21997, 0.6802, -0.69924), (0.00802, 0.71551, 0.69855)-35.90855, 74.39508, -48.20399
11given(0.86338, 0.21575, 0.4561), (-0.20097, -0.68211, 0.70309), (0.4628, -0.69869, -0.54556)-69.95991, -53.67241, 90.09476

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Components

#1: Protein
NADP-DEPENDENT MANNITOL DEHYDROGENASE / MTDH / MANNITOL 2-DEHYDROGENASE [NADP+]


Mass: 28237.947 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AGARICUS BISPORUS (common mushroom) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O93868, mannitol 2-dehydrogenase (NADP+)
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3191 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 47 %
Crystal growpH: 7.5 / Details: 90 MM TRIS-HCL PH 7.5, 18% PEG4000, 9% ISOPROPANOL
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-20 mg/mlprotein1drop
21 mMNADP1drop
390 mMTris-HCl1reservoirpH7.5
418 %PEG40001reservoir
59 %isopropanol1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. obs: 508943 / % possible obs: 98.4 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 11.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 3.1 / % possible all: 97
Reflection
*PLUS
Lowest resolution: 40 Å
Reflection shell
*PLUS
% possible obs: 97 % / Num. unique obs: 173816

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CYD

1cyd


Resolution: 1.5→20 Å / SU B: 1.45 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R Free: 0.07 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.209 5112 1 %RANDOM
Rwork0.193 ---
obs0.193 503641 100 %-
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23424 0 582 3191 27197
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.36

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