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- PDB-3rfx: Crystal structure of uronate dehydrogenase from Agrobacterium tum... -

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Basic information

Entry
Database: PDB / ID: 3rfx
TitleCrystal structure of uronate dehydrogenase from Agrobacterium tumefaciens, Y136A mutant complexed with NAD
ComponentsUronate dehydrogenase
KeywordsOXIDOREDUCTASE / active site mutant / Rossmann fold / NAD
Function / homology
Function and homology information


uronate dehydrogenase / uronate dehydrogenase activity / nucleotide binding
Similarity search - Function
NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Uronate dehydrogenase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsParkkinen, T. / Rouvinen, J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structure of Uronate Dehydrogenase from Agrobacterium tumefaciens.
Authors: Parkkinen, T. / Boer, H. / Janis, J. / Andberg, M. / Penttila, M. / Koivula, A. / Rouvinen, J.
History
DepositionApr 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 17, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uronate dehydrogenase
B: Uronate dehydrogenase
C: Uronate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,11812
Polymers87,5583
Non-polymers2,5609
Water16,141896
1
A: Uronate dehydrogenase
B: Uronate dehydrogenase
C: Uronate dehydrogenase
hetero molecules

A: Uronate dehydrogenase
B: Uronate dehydrogenase
C: Uronate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,23724
Polymers175,1166
Non-polymers5,12018
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area21480 Å2
ΔGint-152 kcal/mol
Surface area56100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.540, 165.540, 174.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-318-

HOH

21A-447-

HOH

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Components

#1: Protein Uronate dehydrogenase


Mass: 29186.078 Da / Num. of mol.: 3 / Mutation: Y136A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / ATCC 33970 / Gene: udh, AGR_L_3333, Atu3143 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q7CRQ0, uronate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 896 / 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: 3.93 Å3/Da / Density % sol: 68.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.8 M ammonium phosphate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 110282 / Num. obs: 107609 / % possible obs: 97.6 %
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 11 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 6.1 / Num. unique all: 7980 / % possible all: 98.9

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RFT

3rft


Resolution: 1.9→47.515 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 16.36
RfactorNum. reflection% reflectionSelection details
Rfree0.1802 5380 5 %RANDOM
Rwork0.1573 ---
obs0.1584 107595 97.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.928 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5074 Å20 Å2-0 Å2
2--2.5074 Å20 Å2
3----5.0147 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6111 0 111 896 7118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076384
X-RAY DIFFRACTIONf_angle_d1.0528712
X-RAY DIFFRACTIONf_dihedral_angle_d19.0612358
X-RAY DIFFRACTIONf_chiral_restr0.074924
X-RAY DIFFRACTIONf_plane_restr0.0051152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.20555380.172410216X-RAY DIFFRACTION99
1.9679-2.04670.20695370.167210209X-RAY DIFFRACTION99
2.0467-2.13990.1995370.160910195X-RAY DIFFRACTION99
2.1399-2.25270.19725370.15610206X-RAY DIFFRACTION98
2.2527-2.39380.18785370.158910209X-RAY DIFFRACTION98
2.3938-2.57860.18865370.159110197X-RAY DIFFRACTION98
2.5786-2.83810.18455360.162510183X-RAY DIFFRACTION98
2.8381-3.24870.18115370.154410198X-RAY DIFFRACTION97
3.2487-4.09270.14695360.139110199X-RAY DIFFRACTION96
4.0927-47.53030.17525480.160310403X-RAY DIFFRACTION94

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