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- PDB-4oqz: Streptomyces aurantiacus imine reductase -

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Basic information

Entry
Database: PDB / ID: 4oqz
TitleStreptomyces aurantiacus imine reductase
ComponentsPutative oxidoreductase YfjR
KeywordsOXIDOREDUCTASE / rossmann fold / NADPH binding
Function / homology
Function and homology information


organic acid catabolic process / NADP binding / oxidoreductase activity
Similarity search - Function
: / NADPH-dependent reductive aminase-like, C-terminal domain / : / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 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 ...: / NADPH-dependent reductive aminase-like, C-terminal domain / : / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 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
Putative oxidoreductase YfjR
Similarity search - Component
Biological speciesStreptomyces aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsSchneider, L.K. / Huber, T. / Gerhardt, S. / Muller, M. / Einsle, O.
CitationJournal: CHEMCATCHEM / Year: 2014
Title: Direct Reductive Amination of Ketones: Structure and Activity of S-Selective Imine Reductases from Streptomyces.
Authors: Huber, T. / Schneider, L. / Prag, A. / Gerhardt, S. / Einsle, O. / Muller, M.
History
DepositionFeb 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Structure summary
Revision 1.2Aug 9, 2017Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative oxidoreductase YfjR


Theoretical massNumber of molelcules
Total (without water)30,4841
Polymers30,4841
Non-polymers00
Water88349
1
A: Putative oxidoreductase YfjR

A: Putative oxidoreductase YfjR


Theoretical massNumber of molelcules
Total (without water)60,9692
Polymers60,9692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area7750 Å2
ΔGint-77 kcal/mol
Surface area22010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.272, 73.964, 166.503
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Putative oxidoreductase YfjR


Mass: 30484.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aurantiacus (bacteria) / Strain: JA 4570 / Gene: STRAU_6765 / Production host: Escherichia coli (E. coli) / References: UniProt: S3Z901
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.2 M MgCl2, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 6, 2013
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.96→48.13 Å / Num. all: 23000 / Num. obs: 22908 / % possible obs: 100 % / Observed criterion σ(F): 22 / Redundancy: 12.6 % / Biso Wilson estimate: 37.05 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 21.5
Reflection shellResolution: 1.96→1.963 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.013 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.01264 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
BUSTER2.10.0refinement
autoPROCdata scaling
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→48.13 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.9293 / SU R Cruickshank DPI: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2496 1167 5.12 %RANDOM
Rwork0.2165 ---
obs0.2182 22784 99.94 %-
all-23000 --
Displacement parametersBiso mean: 64.64 Å2
Baniso -1Baniso -2Baniso -3
1-5.7177 Å20 Å20 Å2
2--0.9631 Å20 Å2
3----6.6807 Å2
Refine analyzeLuzzati coordinate error obs: 0.507 Å
Refinement stepCycle: LAST / Resolution: 1.96→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 0 49 2144
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012137HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.132905HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d704SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes46HARMONIC2
X-RAY DIFFRACTIONt_gen_planes325HARMONIC5
X-RAY DIFFRACTIONt_it2137HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion21.23
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion278SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2477SEMIHARMONIC4
LS refinement shellResolution: 1.96→2.06 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2833 148 4.95 %
Rwork0.2334 2839 -
all0.2358 2987 -
obs--99.94 %
Refinement TLS params.Method: refined / Origin x: -5.0802 Å / Origin y: -16.7514 Å / Origin z: -14.8962 Å
111213212223313233
T-0.5981 Å20.0164 Å20.0586 Å2--0.328 Å2-0.2314 Å2---0.1644 Å2
L2.6144 °2-0.3721 °20.8235 °2-1.3156 °2-0.9008 °2--6.7068 °2
S-0.0036 Å °0.7301 Å °-0.588 Å °-0.3181 Å °-0.3702 Å °-0.2104 Å °0.415 Å °-0.2438 Å °0.3738 Å °
Refinement TLS groupSelection details: { A|3 - A|287 }

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