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- PDB-4im7: Crystal structure of fructuronate reductase (ydfI) from E. coli C... -

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Basic information

Entry
Database: PDB / ID: 4im7
TitleCrystal structure of fructuronate reductase (ydfI) from E. coli CFT073 (EFI TARGET EFI-506389) complexed with NADH and D-mannonate
ComponentsHypothetical oxidoreductase ydfI
KeywordsOXIDOREDUCTASE / rossmann fold / Structural Genomics
Function / homology
Function and homology information


mannitol metabolic process / Oxidoreductases / oxidoreductase activity / nucleotide binding
Similarity search - Function
Mannitol dehydrogenase, conserved site / Mannitol dehydrogenases signature. / Mannitol dehydrogenase / Mannitol dehydrogenase, N-terminal / Mannitol dehydrogenase Rossmann domain / Mannitol dehydrogenase, C-terminal / Mannitol dehydrogenase C-terminal domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 ...Mannitol dehydrogenase, conserved site / Mannitol dehydrogenases signature. / Mannitol dehydrogenase / Mannitol dehydrogenase, N-terminal / Mannitol dehydrogenase Rossmann domain / Mannitol dehydrogenase, C-terminal / Mannitol dehydrogenase C-terminal domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
D-MANNONIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Hypothetical oxidoreductase ydfI / Hypothetical oxidoreductase ydfI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsLukk, T. / Wichelecki, D. / Imker, H.J. / Gerlt, J.A. / Nair, S.K.
CitationJournal: To be Published
Title: Crystal structure of fructuronate reductase (ydfI) from E. coli CFT073 (EFI TARGET EFI-506389) complexed with NADH and D-mannonate
Authors: Wichelecki, S. / Lukk, T. / Imker, H.J. / Nair, S.K. / Gerlt, J.A.
History
DepositionJan 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Structure summary
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Hypothetical oxidoreductase ydfI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8894
Polymers55,9311
Non-polymers9583
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.490, 92.490, 136.000
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Hypothetical oxidoreductase ydfI


Mass: 55931.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CFT073 / Gene: c1968, ydfI / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8FHD0, UniProt: A0A0H2V7F2*PLUS, Oxidoreductases
#2: Chemical ChemComp-CS2 / D-MANNONIC ACID / D-MANNONATE


Mass: 196.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O7
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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 Å3/Da / Density % sol: 59.03 %
Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein solution was at 10 mg/mL containing 20 mM Tris (pH 7.5) and 100 mM NaCl. Mother liqueur contained 1.7 M ammonium sulfate, 0.085 M Hepes (pH 7.5), 1.7% PEG 400 and 15% glycerol, vapor ...Details: Protein solution was at 10 mg/mL containing 20 mM Tris (pH 7.5) and 100 mM NaCl. Mother liqueur contained 1.7 M ammonium sulfate, 0.085 M Hepes (pH 7.5), 1.7% PEG 400 and 15% glycerol, vapor diffusion, sitting drop, temperature 282K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 2, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 53597 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.297 Å2 / Rsym value: 0.09 / Net I/σ(I): 11.42
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.9-1.950.6112.55298027589199.9
1.95-20.4923.11292947454199.8
2-2.060.4073.76281537159199.9
2.06-2.120.3084.74274786977199.9
2.12-2.190.2555.51267396782199.9
2.19-2.270.2116.5256976504199.9
2.27-2.360.1787.53250676332199.9
2.36-2.450.168.3240446072199.9
2.45-2.560.1359.56230995835199.9
2.56-2.690.11810.86221055584199.9
2.69-2.830.09912.472098752951100
2.83-30.08114.64198164999199.9
3-3.210.06717.94185414696199.9
3.21-3.470.05521.54172114382199.9
3.47-3.80.04824.13157544025199.9
3.8-4.250.04226.65143033654199.9
4.25-4.910.03928.351256032181100
4.91-6.010.03927.131060727011100
6.01-8.50.03728.38833121201100
8.5-300.03332.6342051109197.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.551 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.9156 / SU ML: 0.17 / σ(F): 2.02 / Phase error: 15.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1728 2679 5 %random
Rwork0.1484 ---
obs0.1496 53593 99.94 %-
all-53647 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.397 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso max: 88.32 Å2 / Biso mean: 23.6144 Å2 / Biso min: 7.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.0825 Å2-0 Å20 Å2
2---0.0825 Å2-0 Å2
3---0.165 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3758 0 62 471 4291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073914
X-RAY DIFFRACTIONf_angle_d1.1055338
X-RAY DIFFRACTIONf_chiral_restr0.072605
X-RAY DIFFRACTIONf_plane_restr0.004684
X-RAY DIFFRACTIONf_dihedral_angle_d151417
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9001-1.93460.25141400.209226662806
1.9346-1.97180.2441390.198626392778
1.9718-2.01210.24951390.187126452784
2.0121-2.05580.21081400.167626602800
2.0558-2.10360.18671390.159326362775
2.1036-2.15620.19791390.145926342773
2.1562-2.21450.17311390.14426482787
2.2145-2.27960.1931390.140426422781
2.2796-2.35320.18431410.138726882829
2.3532-2.43730.1791400.141626482788
2.4373-2.53480.17571400.142126712811
2.5348-2.65010.16441410.14626652806
2.6501-2.78970.1781400.148626752815
2.7897-2.96430.19121410.162226732814
2.9643-3.1930.16531420.155727052847
3.193-3.51380.15391420.148126902832
3.5138-4.02120.14941440.130927272871
4.0212-5.06220.13231440.11927352879
5.0622-29.55470.16011500.157928673017
Refinement TLS params.Method: refined / Origin x: 33.4822 Å / Origin y: 15.9306 Å / Origin z: 15.1891 Å
111213212223313233
T0.0547 Å20.0034 Å2-0.0065 Å2-0.1041 Å20.0096 Å2--0.086 Å2
L0.0278 °20.0142 °2-0.0325 °2-0.5388 °2-0.3668 °2--0.6489 °2
S-0.0037 Å °0.009 Å °0.0071 Å °-0.0505 Å °0.0575 Å °0.0408 Å °0.0631 Å °-0.0376 Å °0.0085 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 487
2X-RAY DIFFRACTION1allA1 - 501
3X-RAY DIFFRACTION1allA1 - 502
4X-RAY DIFFRACTION1allA1 - 503
5X-RAY DIFFRACTION1allA1 - 1071

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