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- PDB-7x2y: Crystal Structure of cis-4,5-dihydrodiol phthalate dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 7x2y
TitleCrystal Structure of cis-4,5-dihydrodiol phthalate dehydrogenase in complex with NAD+ and 3-Hydroxybenzoate
Components4,5-dihydroxyphthalate dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / bacterial protein / NAD cofactor
Function / homology3-HYDROXYBENZOIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION
Function and homology information
Biological speciesComamonas testosteroni KF-1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsSharma, M. / Mahto, J.K. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)DST/TMD/EWO/WTI/2K19/EWFH/2019/8 (G) India
CitationJournal: Arch.Biochem.Biophys. / Year: 2022
Title: Conformational flexibility enables catalysis of phthalate cis-4,5-dihydrodiol dehydrogenase.
Authors: Mahto, J.K. / Sharma, M. / Neetu, N. / Kayastha, A. / Aggarwal, S. / Kumar, P.
History
DepositionFeb 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4,5-dihydroxyphthalate dehydrogenase
B: 4,5-dihydroxyphthalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,98419
Polymers86,0932
Non-polymers2,89017
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-43 kcal/mol
Surface area25070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.579, 88.315, 162.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 4 - 391 / Label seq-ID: 4 - 391

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 4,5-dihydroxyphthalate dehydrogenase


Mass: 43046.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni KF-1 (bacteria) / Gene: O987_21845 / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 6 types, 351 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-3HB / 3-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium phosphate dibasic, and 20 % polyethylene glycol 3350, 100 mM Tris buffer pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Dec 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.48→27.18 Å / Num. obs: 28203 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.994 / Net I/σ(I): 11.6
Reflection shellResolution: 2.48→2.54 Å / Num. unique obs: 3138 / CC1/2: 0.904 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MOI

3moi


Resolution: 2.48→27.18 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.844 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.646 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2351 1412 5 %RANDOM
Rwork0.1921 ---
obs0.1943 26742 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.95 Å2 / Biso mean: 21.005 Å2 / Biso min: 0.86 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å2-0 Å2
2--3.72 Å2-0 Å2
3----2.64 Å2
Refinement stepCycle: final / Resolution: 2.48→27.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5336 0 190 334 5860
Biso mean--41.77 22.4 -
Num. residues----684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125659
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.6327674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2895678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.85120.44318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.76315848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3751554
X-RAY DIFFRACTIONr_chiral_restr0.1160.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024364
Refine LS restraints NCS

Ens-ID: 1 / Number: 11307 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.48→2.544 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 115 -
Rwork0.231 1937 -
all-2052 -
obs--99.76 %

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