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- PDB-5uhz: Crystal Structure of an Oxidoreductase from Agrobacterium radioba... -

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Basic information

Entry
Database: PDB / ID: 5uhz
TitleCrystal Structure of an Oxidoreductase from Agrobacterium radiobacter in Complex with NAD+, D-Apionate and Magnesium
ComponentsOxidoreductase protein
KeywordsOXIDOREDUCTASE / D-Apionate
Function / homology
Function and homology information


D-apiose dehydrogenase / oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
: / : / GFO/IDH/MocA C-terminal domain / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-89Y / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / D-apiose dehydrogenase
Similarity search - Component
Biological speciesAgrobacterium radiobacter (Agrobacterium genomosp. 4)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCook, W.J. / Fedorov, A.A. / Fedorov, E.V. / Huang, H. / Bonanno, J.B. / Gerlt, J.A. / Almo, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To be published
Title: Crystal Structure of an Oxidoreductase from Agrobacterium radiobacter in Complex with NAD+, D-Apionate and Magnesium
Authors: Cook, W.J. / Fedorov, A.A. / Fedorov, E.V. / Huang, H. / Bonanno, J.B. / Gerlt, J.A. / Almo, S.C.
History
DepositionJan 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Structure summary
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0May 13, 2020Group: Atomic model / Category: atom_site / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / struct_conn ...chem_comp / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.type / _struct_conn.pdbx_dist_value ..._chem_comp.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase protein
B: Oxidoreductase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6478
Polymers74,9752
Non-polymers1,6726
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-38 kcal/mol
Surface area24540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.763, 114.183, 66.158
Angle α, β, γ (deg.)90.00, 94.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Oxidoreductase protein


Mass: 37487.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium radiobacter (strain K84 / ATCC BAA-868) (bacteria)
Strain: K84 / ATCC BAA-868 / Gene: Arad_9238 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B9JK80
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Sugar ChemComp-89Y / (3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-one


Type: D-saccharide / Mass: 148.114 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O5
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 3.48 Å3/Da / Density % sol: 64.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.5 M Sodium formate, 5 mM NAD+, 5 mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2016 / Details: Diamond
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.2→29.57 Å / Num. obs: 51035 / % possible obs: 98.2 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.039 / Rrim(I) all: 0.058 / Net I/σ(I): 6.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7372 / CC1/2: 0.795 / Rpim(I) all: 0.596 / Rrim(I) all: 0.891 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
Aimless0.5.21data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UHW

5uhw


Resolution: 2.2→29.57 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 15.086 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 2486 5 %RANDOM
Rwork0.19996 ---
obs0.20126 47565 96.32 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.078 Å2
Baniso -1Baniso -2Baniso -3
1--2.49 Å2-0 Å21.77 Å2
2--1.64 Å2-0 Å2
3---0.53 Å2
Refinement stepCycle: 1 / Resolution: 2.2→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5158 0 110 108 5376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195382
X-RAY DIFFRACTIONr_bond_other_d0.0010.024882
X-RAY DIFFRACTIONr_angle_refined_deg1.231.9637328
X-RAY DIFFRACTIONr_angle_other_deg0.883311278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5445682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59324.035228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77615822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1391532
X-RAY DIFFRACTIONr_chiral_restr0.0650.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026036
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021126
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5643.5132734
X-RAY DIFFRACTIONr_mcbond_other1.5643.5122733
X-RAY DIFFRACTIONr_mcangle_it2.5045.2643414
X-RAY DIFFRACTIONr_mcangle_other2.5045.2663415
X-RAY DIFFRACTIONr_scbond_it1.8433.7972648
X-RAY DIFFRACTIONr_scbond_other1.843.7972648
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9345.6213915
X-RAY DIFFRACTIONr_long_range_B_refined4.98842.1395803
X-RAY DIFFRACTIONr_long_range_B_other4.9842.0745793
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 123 -
Rwork0.389 2658 -
obs--75.51 %
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)
11.08560.2769-0.35211.25990.42761.50690.2812-0.27980.01860.2927-0.2864-0.13840.13480.15920.00520.2015-0.1495-0.08140.27070.07620.08418.1988-31.374115.3137
21.0179-1.3027-0.53821.93530.48351.02630.36380.4597-0.0803-0.3073-0.4445-0.019-0.0183-0.07690.08080.29720.3084-0.13830.4914-0.02240.164924.3305-56.1416-19.792
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 345
2X-RAY DIFFRACTION2B4 - 345

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