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- PDB-4ur8: Crystal structure of keto-deoxy-D-galactarate dehydratase complex... -

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Basic information

Entry
Database: PDB / ID: 4ur8
TitleCrystal structure of keto-deoxy-D-galactarate dehydratase complexed with 2-oxoadipic acid
ComponentsKETO-DEOXY-D-GALACTARATE DEHYDRATASE
KeywordsLYASE / DECARBOXYLATE / DEHYDRATASE / BIOCATALYSIS / OXIDATIVE PATHWAY / D-GALACTURONIC ACID
Function / homology
Function and homology information


5-dehydro-4-deoxyglucarate dehydratase / 5-dehydro-4-deoxyglucarate dehydratase activity / D-glucarate catabolic process / 4-hydroxy-tetrahydrodipicolinate synthase activity
Similarity search - Function
5-dehydro-4-deoxyglucarate dehydratase / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / 2-OXOADIPIC ACID / Probable 5-dehydro-4-deoxyglucarate dehydratase
Similarity search - Component
Biological speciesAGROBACTERIUM TUMEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.097 Å
AuthorsTaberman, H. / Parkkinen, T. / Hakulinen, N. / Rouvinen, J.
CitationJournal: Biochemistry / Year: 2014
Title: Structure and Function of a Decarboxylating Agrobacterium Tumefaciens Keto-Deoxy-D-Galactarate Dehydratase.
Authors: Taberman, H. / Andberg, M.B. / Parkkinen, T. / Janis, J. / Penttila, M. / Hakulinen, N. / Koivula, A. / Rouvinen, J.
History
DepositionJun 26, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jan 28, 2015Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Other
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KETO-DEOXY-D-GALACTARATE DEHYDRATASE
B: KETO-DEOXY-D-GALACTARATE DEHYDRATASE
C: KETO-DEOXY-D-GALACTARATE DEHYDRATASE
D: KETO-DEOXY-D-GALACTARATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,98210
Polymers134,2494
Non-polymers7336
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11860 Å2
ΔGint-60.2 kcal/mol
Surface area39350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.520, 119.030, 74.280
Angle α, β, γ (deg.)90.00, 112.24, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
KETO-DEOXY-D-GALACTARATE DEHYDRATASE / 5-KETO-4-DEOXY-GLUCARATE DEHYDRATASE / KDGDH


Mass: 33562.363 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AGROBACTERIUM TUMEFACIENS (bacteria) / Plasmid: PBAT4-ATKDG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8UB77, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical
ChemComp-OOG / 2-OXOADIPIC ACID


Mass: 160.125 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O5
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 8.5 / Details: BICINE PH 8.5, SODIUM FORMATE, PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 8, 2013 / Details: MIRRORS
RadiationMonochromator: SINGLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 76785 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.4
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UR5

4ur5
PDB Unreleased entry


Resolution: 2.097→47.883 Å / SU ML: 0.33 / σ(F): 1.37 / Phase error: 29.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2721 3838 5 %
Rwork0.2207 --
obs0.2232 76762 96.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.5 Å2
Refinement stepCycle: LAST / Resolution: 2.097→47.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9144 0 46 400 9590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099393
X-RAY DIFFRACTIONf_angle_d1.1712705
X-RAY DIFFRACTIONf_dihedral_angle_d14.8493379
X-RAY DIFFRACTIONf_chiral_restr0.0451409
X-RAY DIFFRACTIONf_plane_restr0.0061663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0965-2.1230.44251330.36152538X-RAY DIFFRACTION89
2.123-2.1510.37411400.34722648X-RAY DIFFRACTION96
2.151-2.18050.38911420.31952707X-RAY DIFFRACTION96
2.1805-2.21160.34811420.30492687X-RAY DIFFRACTION97
2.2116-2.24460.35091430.2842735X-RAY DIFFRACTION97
2.2446-2.27970.28071430.27882712X-RAY DIFFRACTION97
2.2797-2.31710.30711430.26172732X-RAY DIFFRACTION97
2.3171-2.3570.34211430.24452714X-RAY DIFFRACTION98
2.357-2.39990.31731450.22832742X-RAY DIFFRACTION98
2.3999-2.4460.27081430.22492722X-RAY DIFFRACTION98
2.446-2.4960.2971460.21242776X-RAY DIFFRACTION98
2.496-2.55020.26921440.21612746X-RAY DIFFRACTION98
2.5502-2.60950.27721440.2292728X-RAY DIFFRACTION97
2.6095-2.67480.31871440.2272742X-RAY DIFFRACTION97
2.6748-2.74710.31031430.22842715X-RAY DIFFRACTION97
2.7471-2.82790.27691400.24172650X-RAY DIFFRACTION95
2.8279-2.91920.29011210.22722311X-RAY DIFFRACTION83
2.9192-3.02350.25011430.22162707X-RAY DIFFRACTION96
3.0235-3.14460.25691460.22442782X-RAY DIFFRACTION98
3.1446-3.28760.26091450.22542746X-RAY DIFFRACTION98
3.2876-3.46090.28331470.21612795X-RAY DIFFRACTION98
3.4609-3.67770.27051440.21642731X-RAY DIFFRACTION98
3.6777-3.96150.29711470.20442795X-RAY DIFFRACTION98
3.9615-4.35990.21311440.18812747X-RAY DIFFRACTION97
4.3599-4.99030.22811420.17822695X-RAY DIFFRACTION96
4.9903-6.2850.24321310.2012483X-RAY DIFFRACTION88
6.285-47.89540.19451500.18042838X-RAY DIFFRACTION98

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