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

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Basic information

Entry
Database: PDB / ID: 7wzd
TitleCrystal Structure of cis-4,5-dihydrodiol phthalate dehydrogenase from Comamonas testosteroni KF1
Components4,5-dihydroxyphthalate dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / bacterial protein / NAD cofactor
Biological speciesComamonas testosteroni KF-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 17, 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

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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)86,3705
Polymers86,0932
Non-polymers2763
Water8,701483
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-28 kcal/mol
Surface area26620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.177, 90.696, 164.110
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

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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.2 M Ammonium phosphate dibasic, 100 mM Tris buffer pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.8→60.92 Å / Num. obs: 19666 / % possible obs: 95.5 % / Redundancy: 1.8 % / CC1/2: 0.943 / Net I/σ(I): 6.2
Reflection shellResolution: 2.8→2.95 Å / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2737 / CC1/2: 0.832

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Processing

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

3moi


Resolution: 2.8→60.92 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.895 / SU B: 15.934 / SU ML: 0.299 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.2 / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 965 4.9 %RANDOM
Rwork0.1909 ---
obs0.1944 18701 95.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.04 Å2 / Biso mean: 20.439 Å2 / Biso min: 0.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0 Å2
2--0.1 Å20 Å2
3---0.12 Å2
Refinement stepCycle: final / Resolution: 2.8→60.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5351 0 18 483 5852
Biso mean--28.35 20.5 -
Num. residues----684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125505
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.637472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7625678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.91320.25320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.67415854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4191556
X-RAY DIFFRACTIONr_chiral_restr0.1290.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024284
Refine LS restraints NCS

Ens-ID: 1 / Number: 10926 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 58 -
Rwork0.253 1261 -
all-1319 -
obs--88.11 %

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