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- PDB-7x1x: Crystal Structure of cis-4,5-dihydrodiol phthalate dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 7x1x
TitleCrystal Structure of cis-4,5-dihydrodiol phthalate dehydrogenase in complex with NAD+
Components4,5-dihydroxyphthalate dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / bacterial protein / NAD cofactor
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesComamonas testosteroni KF-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 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 24, 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)87,6967
Polymers86,0932
Non-polymers1,6035
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-36 kcal/mol
Surface area25620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.070, 92.070, 163.230
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: 0 / 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: 0 / 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.2M AMMONIUM PHOSPHATE DIBASIC, 100mM TRIS BUFFER pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.77→46.89 Å / Num. obs: 21448 / % possible obs: 99.9 % / Redundancy: 1.9 % / CC1/2: 0.99 / Net I/σ(I): 12.5
Reflection shellResolution: 2.77→2.92 Å / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3070 / CC1/2: 0.93

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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: 2.77→46.89 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.911 / SU B: 42 / SU ML: 0.374 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.408 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2779 1083 5 %RANDOM
Rwork0.2186 ---
obs0.2215 20365 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.65 Å2 / Biso mean: 58.478 Å2 / Biso min: 21.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å20 Å20 Å2
2--4.94 Å2-0 Å2
3----3.44 Å2
Refinement stepCycle: final / Resolution: 2.77→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5256 0 106 149 5511
Biso mean--83.83 51.77 -
Num. residues----676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125505
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.6317493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7555670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.32120.588306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.0615828
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7081550
X-RAY DIFFRACTIONr_chiral_restr0.1160.2686
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024276
Refine LS restraints NCS

Ens-ID: 1 / Number: 11222 / 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: 2.77→2.842 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.301 71 -
Rwork0.301 1494 -
obs--99.75 %
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)
12.2865-0.3003-2.02860.13350.52624.52280.03970.0689-0.06640.00910.013-0.0670.10540.1409-0.05270.00830.0015-0.00830.260.0030.06869.98942.595-39.4809
22.37180.2137-2.02110.1343-0.52074.46410.005-0.0234-0.0888-0.01930.05670.0620.0993-0.2295-0.06170.0045-0.0127-0.01020.227-0.00460.0559-9.92622.5058-2.6734
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 391
2X-RAY DIFFRACTION2B4 - 391

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