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- PDB-1p4c: High Resolution Structure of Oxidized Active Mutant of (S)-Mandel... -

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Basic information

Entry
Database: PDB / ID: 1p4c
TitleHigh Resolution Structure of Oxidized Active Mutant of (S)-Mandelate Dehydrogenase
ComponentsL(+)-Mandelate Dehydrogenase
KeywordsOXIDOREDUCTASE / TIM BARREL / Hydroxy acid oxidizing enzyme
Function / homology
Function and homology information


(S)-mandelate dehydrogenase / (S)-mandelate dehydrogenase activity / oxidative photosynthetic carbon pathway / (S)-2-hydroxy-acid oxidase / (S)-2-hydroxy-acid oxidase activity / mandelate catabolic process / response to other organism / L-lactate dehydrogenase (NAD+) activity / aerobic respiration / peroxisome ...(S)-mandelate dehydrogenase / (S)-mandelate dehydrogenase activity / oxidative photosynthetic carbon pathway / (S)-2-hydroxy-acid oxidase / (S)-2-hydroxy-acid oxidase activity / mandelate catabolic process / response to other organism / L-lactate dehydrogenase (NAD+) activity / aerobic respiration / peroxisome / FMN binding / plasma membrane
Similarity search - Function
Alpha-hydroxy acid dehydrogenase, FMN-dependent / FMN-dependent alpha-hydroxy acid dehydrogenase, active site / FMN hydroxy acid dehydrogenase domain / FMN-dependent alpha-hydroxy acid dehydrogenases active site. / FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Alpha-hydroxy acid dehydrogenase, FMN-dependent / FMN-dependent alpha-hydroxy acid dehydrogenase, active site / FMN hydroxy acid dehydrogenase domain / FMN-dependent alpha-hydroxy acid dehydrogenases active site. / FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Glycolate oxidase / (S)-mandelate dehydrogenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
Spinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSukumar, N. / Mitra, B. / Mathews, F.S.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: High Resolution Structures of an Oxidized and Reduced Flavoprotein: THE WATER SWITCH IN A SOLUBLE FORM OF (S)-MANDELATE DEHYDROGENASE
Authors: Sukumar, N. / Dewanti, A.R. / Mitra, B. / Mathews, F.S.
#1: Journal: Biochemistry / Year: 2001
Title: Structure of an active Soluble Mutant of the Membrane- Associated (S)-Mandelate Dehydrogenase
Authors: Sukumar, N. / Xu, Y. / Gatti, D.L. / Mitra, B. / Mathews, F.S.
History
DepositionApr 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2017Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Chimeric mutant of (s)-mandelate dehydrogenase with residues 177-196 replaced by residues ...SEQUENCE Chimeric mutant of (s)-mandelate dehydrogenase with residues 177-196 replaced by residues 176- 195 of glycolate oxidase. The authors believe that SwissProt entry P20932 incorrectly lists residue 15 as ARG instead of ALA. Sequencing of (s)-mandelate dehydrogenase, as well as of the original clone pSCR4, has been done a number of times including site-specific mutants and has repeatedly confirmed that it is ALA 15 rather than ARG 15.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L(+)-Mandelate Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8804
Polymers42,1321
Non-polymers7483
Water7,206400
1
A: L(+)-Mandelate Dehydrogenase
hetero molecules

A: L(+)-Mandelate Dehydrogenase
hetero molecules

A: L(+)-Mandelate Dehydrogenase
hetero molecules

A: L(+)-Mandelate Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,52016
Polymers168,5294
Non-polymers2,99112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-y+2,x,z1
crystal symmetry operation4_575y,-x+2,z1
Buried area16660 Å2
ΔGint-120 kcal/mol
Surface area50210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)99.400, 99.400, 87.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein L(+)-Mandelate Dehydrogenase / S-MANDELATE DEHYDROGENASE / MDH


Mass: 42132.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 20 RESIDUE SUBSTITUTION FROM GLYCOLATE OXIDASE AT RESIDUE 177
Source: (gene. exp.) Pseudomonas putida (bacteria), (gene. exp.) Spinacia oleracea (spinach)
Production host: Escherichia coli (E. coli) / References: UniProt: P20932, UniProt: P05414
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.56 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: ammonium sulfate, ethylene glycol, FMN, Sodium Chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Sukumar, N., (2001) Biochemistry, 40, 9870.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110-15 mg/mlprotein1drop
20.2 MMES1drop
30.75 %ammonium sulfate1drop
410 %ethylene glycol1drop
50.020 mMFMN1drop
64.0 M1reservoir1mlNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97625 Å
DetectorType: CUSTOM-MADE / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 92753 / % possible obs: 99.8 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.059
Reflection shellResolution: 1.35→1.4 Å / Rmerge(I) obs: 0.279 / % possible all: 98.1
Reflection
*PLUS
Lowest resolution: 500 Å / Num. obs: 91731 / Redundancy: 5.1 % / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 99.1 % / Rmerge(I) obs: 0.282

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HUV

1huv


Resolution: 1.35→39.6 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 240668.51 / Data cutoff high rms absF: 240668.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.194 8965 10 %RANDOM
Rwork0.184 ---
obs0.184 89649 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.3837 Å2 / ksol: 0.352965 e/Å3
Displacement parametersBiso mean: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.15 Å20 Å20 Å2
2--2.15 Å20 Å2
3----4.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.35→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2747 0 48 400 3195
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.951.5
X-RAY DIFFRACTIONc_mcangle_it1.522
X-RAY DIFFRACTIONc_scbond_it1.622
X-RAY DIFFRACTIONc_scangle_it2.42.5
LS refinement shellResolution: 1.35→1.4 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.261 1367 9.9 %
Rwork0.244 12400 -
obs--89.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FMN.PARFMN.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMLIGANDS.TOP
X-RAY DIFFRACTION4LIGANDS.PARWATER.TOP
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.54
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96

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