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- PDB-5a05: Crystal structure of aldose-aldose oxidoreductase from Caulobacte... -

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Basic information

Entry
Database: PDB / ID: 5a05
TitleCrystal structure of aldose-aldose oxidoreductase from Caulobacter crescentus complexed with maltotriose
ComponentsALDOSE-ALDOSE OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Glucose-fructose oxidoreductase, bacterial / : / Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...Glucose-fructose oxidoreductase, bacterial / : / Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-maltotriose / MALONATE ION / Chem-NDP / Glucose-fructose oxidoreductase
Similarity search - Component
Biological speciesCAULOBACTER CRESCENTUS CB15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.897 Å
AuthorsTaberman, H. / Rouvinen, J. / Parkkinen, T.
CitationJournal: Biochem.J. / Year: 2015
Title: Structure and Function of Caulobacter Crescentus Aldose-Aldose Oxidoreductase.
Authors: Taberman, H. / Andberg, M. / Koivula, A. / Hakulinen, N. / Penttila, M. / Rouvinen, J. / Parkkinen, T.
History
DepositionApr 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: ALDOSE-ALDOSE OXIDOREDUCTASE
B: ALDOSE-ALDOSE OXIDOREDUCTASE
C: ALDOSE-ALDOSE OXIDOREDUCTASE
D: ALDOSE-ALDOSE OXIDOREDUCTASE
E: ALDOSE-ALDOSE OXIDOREDUCTASE
F: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,53319
Polymers223,7376
Non-polymers6,79613
Water32,9671830
1
A: ALDOSE-ALDOSE OXIDOREDUCTASE
E: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0796
Polymers74,5792
Non-polymers2,5004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint10.2 kcal/mol
Surface area24410 Å2
MethodPISA
2
C: ALDOSE-ALDOSE OXIDOREDUCTASE
F: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6766
Polymers74,5792
Non-polymers2,0974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint5.1 kcal/mol
Surface area24480 Å2
MethodPISA
3
B: ALDOSE-ALDOSE OXIDOREDUCTASE
D: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7787
Polymers74,5792
Non-polymers2,1995
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint6.1 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.295, 151.321, 108.693
Angle α, β, γ (deg.)90.00, 108.66, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.0196, -0.818, 0.5749), (0.8315, -0.3327, -0.445), (0.5552, 0.4693, 0.6866)21.938, -8.1847, -18.0015
2given(0.1805, -0.6783, -0.7122), (-0.7539, -0.5605, 0.3427), (-0.6317, 0.4751, -0.612)72.5255, 23.7418, 62.8782
3given(0.1784, 0.7342, -0.655), (0.6681, -0.5791, -0.4672), (-0.7223, -0.3543, -0.5939)59.4233, -2.2656, 66.2573
4given(-0.9779, 0.2081, -0.0187), (0.2072, 0.9538, -0.2177), (-0.0275, -0.2167, -0.9758)82.2432, -3.4327, 47.272
5given(-0.3175, 0.5383, 0.7807), (-0.5409, -0.779, 0.3172), (0.7789, -0.3215, 0.5385)14.8164, 20.2807, -21.0747

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Components

#1: Protein
ALDOSE-ALDOSE OXIDOREDUCTASE


Mass: 37289.438 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAULOBACTER CRESCENTUS CB15 (bacteria) / Strain: CB15 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q9A8X3*PLUS, EC: 1.1.99.-
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1830 / 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: 3.5 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 6.5 / Details: MES PH 6.5, AMMONIUM SULPHATE, 2-PROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2014 / Details: MIRRORS
RadiationMonochromator: CHANNEL-CUT SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 239445 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 23.42 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.1 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H6A

1h6a


Resolution: 1.897→48.745 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 17.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1781 11973 5 %
Rwork0.1522 --
obs0.1535 239426 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26 Å2
Refinement stepCycle: LAST / Resolution: 1.897→48.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15558 0 445 1830 17833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716390
X-RAY DIFFRACTIONf_angle_d1.11222284
X-RAY DIFFRACTIONf_dihedral_angle_d12.9596143
X-RAY DIFFRACTIONf_chiral_restr0.0472446
X-RAY DIFFRACTIONf_plane_restr0.0052905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8969-1.91850.33823650.3066930X-RAY DIFFRACTION91
1.9185-1.94110.29544020.24827637X-RAY DIFFRACTION99
1.9411-1.96470.26343990.22357572X-RAY DIFFRACTION99
1.9647-1.98960.23943960.21277540X-RAY DIFFRACTION99
1.9896-2.01580.22324000.20427600X-RAY DIFFRACTION99
2.0158-2.04340.22724020.19517631X-RAY DIFFRACTION99
2.0434-2.07260.19613980.18557554X-RAY DIFFRACTION99
2.0726-2.10350.22863990.18537587X-RAY DIFFRACTION99
2.1035-2.13640.22484020.18057639X-RAY DIFFRACTION99
2.1364-2.17140.19173980.16767557X-RAY DIFFRACTION99
2.1714-2.20890.20884000.1657601X-RAY DIFFRACTION99
2.2089-2.2490.19613960.16597527X-RAY DIFFRACTION99
2.249-2.29230.20483970.16437536X-RAY DIFFRACTION98
2.2923-2.33910.18534000.15937598X-RAY DIFFRACTION99
2.3391-2.390.19674010.15697635X-RAY DIFFRACTION99
2.39-2.44550.20254000.15997601X-RAY DIFFRACTION99
2.4455-2.50670.19853990.15997576X-RAY DIFFRACTION99
2.5067-2.57450.18334010.16227619X-RAY DIFFRACTION99
2.5745-2.65020.18624040.16437666X-RAY DIFFRACTION100
2.6502-2.73580.19424000.16747611X-RAY DIFFRACTION100
2.7358-2.83350.19634000.16637599X-RAY DIFFRACTION99
2.8335-2.9470.20184000.17667595X-RAY DIFFRACTION99
2.947-3.08110.19584010.16757623X-RAY DIFFRACTION100
3.0811-3.24350.17594020.15287638X-RAY DIFFRACTION100
3.2435-3.44660.15514010.13367607X-RAY DIFFRACTION99
3.4466-3.71270.154020.12277644X-RAY DIFFRACTION99
3.7127-4.08610.13284000.11277606X-RAY DIFFRACTION99
4.0861-4.6770.11133980.10227559X-RAY DIFFRACTION98
4.677-5.89090.13814040.12097671X-RAY DIFFRACTION99
5.8909-48.76120.16124060.14117694X-RAY DIFFRACTION99

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