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- PDB-4d3f: BcSIRED from Bacillus cereus in complex with NADPH -

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Basic information

Entry
Database: PDB / ID: 4d3f
TitleBcSIRED from Bacillus cereus in complex with NADPH
ComponentsIMINE REDUCTASE
KeywordsOXIDOREDUCTASE / IMINE
Function / homologyN-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesBACILLUS CEREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsMan, H. / Hart, S. / Turkenburg, J.P. / Grogan, G.
CitationJournal: Chembiochem / Year: 2015
Title: Structure, Activity and Stereoselectivity of Nadph-Dependent Oxidoreductases Catalysing the S-Selective Reduction of the Imine Substrate 2-Methylpyrroline.
Authors: Man, H. / Wells, E. / Hussain, S. / Leipold, F. / Hart, S. / Turkenburg, J.P. / Turner, N.J. / Grogan, G.
History
DepositionOct 21, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2May 13, 2015Group: Database references
Revision 1.3Sep 18, 2019Group: Data collection / Database references / Source and taxonomy
Category: entity_src_gen / struct_ref / struct_ref_seq
Item: _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num ..._entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: IMINE REDUCTASE
B: IMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6803
Polymers67,9372
Non-polymers7431
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9320 Å2
ΔGint-77.3 kcal/mol
Surface area22120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.230, 62.780, 214.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.7563, -0.6046, 0.2499), (-0.6326, 0.5785, -0.515), (0.1668, -0.5476, -0.82)
Vector: -16.57, -20.97, -42.71)

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Components

#1: Protein IMINE REDUCTASE


Mass: 33968.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Strain: BAG3X2 / Plasmid: PETYSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: dihydrofolate reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 3.2 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growpH: 7.5
Details: 30% (W/V) PEG 3350; 0.2M MGCL2; 0.1M HEPES PH 7.5; PROTEIN AT 50 MG ML-1

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.81→107.25 Å / Num. obs: 69092 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 18.8
Reflection shellResolution: 1.81→1.86 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
xia2data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZGY

3zgy


Resolution: 1.81→107.25 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.432 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 3365 4.9 %RANDOM
Rwork0.17236 ---
obs0.17356 65636 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.734 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20 Å2
2--2.35 Å20 Å2
3----1.59 Å2
Refinement stepCycle: LAST / Resolution: 1.81→107.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4360 0 48 355 4763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0194518
X-RAY DIFFRACTIONr_bond_other_d0.0060.024206
X-RAY DIFFRACTIONr_angle_refined_deg1.9981.9696160
X-RAY DIFFRACTIONr_angle_other_deg1.42739649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6875575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72223.656186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05115707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.1081526
X-RAY DIFFRACTIONr_chiral_restr0.1580.2709
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215122
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021029
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_it2.6032.8042294
X-RAY DIFFRACTIONr_mcbond_other2.5952.8022293
X-RAY DIFFRACTIONr_mcangle_it3.2224.1862865
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.4333.2822224
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 233 -
Rwork0.27 4845 -
obs--99.88 %

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