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- PDB-7wxe: Crystal Structure of Imine Reductase from Paenibacillus mucilaginosus -

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Basic information

Entry
Database: PDB / ID: 7wxe
TitleCrystal Structure of Imine Reductase from Paenibacillus mucilaginosus
Components6-phosphogluconate dehydrogenase
KeywordsOXIDOREDUCTASE / Imine Reductase
Function / homology3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / NADP binding / oxidoreductase activity / NAD(P)-binding domain superfamily / 6-phosphogluconate dehydrogenase
Function and homology information
Biological speciesPaenibacillus mucilaginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWu, K.
Funding support China, 1items
OrganizationGrant numberCountry
Shanghai University of Medicine & Health Sciences China
CitationJournal: To Be Published
Title: Crystal Structure of Imine Reductase from Paenibacillus mucilaginosus
Authors: Wu, K.
History
DepositionFeb 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / struct_ncs_dom_lim / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-phosphogluconate dehydrogenase
B: 6-phosphogluconate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)67,1042
Polymers67,1042
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-76 kcal/mol
Surface area22610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.771, 133.771, 62.230
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 23 through 144 or resid 149 through 306))
d_2ens_1(chain "B" and (resid 23 through 51 or resid 57 through 306))

NCS oper: (Code: givenMatrix: (-0.98327963315, -0.00195843130667, -0.182091536263), (0.0749371649661, -0.91570332468, -0.394806082116), (-0.165968624561, -0.401850203081, 0.900539188456)Vector: 73. ...NCS oper: (Code: given
Matrix: (-0.98327963315, -0.00195843130667, -0.182091536263), (0.0749371649661, -0.91570332468, -0.394806082116), (-0.165968624561, -0.401850203081, 0.900539188456)
Vector: 73.1804712396, -96.5939885712, -13.6547634057)

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Components

#1: Protein 6-phosphogluconate dehydrogenase


Mass: 33551.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus mucilaginosus (bacteria) / Gene: B2K_07400 / Production host: Escherichia coli (E. coli) / References: UniProt: I0BDU9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammouim sulfate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 43954 / % possible obs: 99.8 % / Redundancy: 12.6 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.043 / Net I/σ(I): 12.8
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 2 / Num. unique obs: 1963 / Rpim(I) all: 0.421 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D3F

4d3f


Resolution: 2.5→28.96 Å / SU ML: 0.2369 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.3822
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2489 2871 6.82 %
Rwork0.2059 39209 -
obs0.2089 42080 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.52 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 0 138 4434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00864386
X-RAY DIFFRACTIONf_angle_d1.0275960
X-RAY DIFFRACTIONf_chiral_restr0.055681
X-RAY DIFFRACTIONf_plane_restr0.0077767
X-RAY DIFFRACTIONf_dihedral_angle_d20.4571570
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.29485798619 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.540.27271400.21391835X-RAY DIFFRACTION99.9
2.54-2.580.29791520.21471962X-RAY DIFFRACTION99.91
2.58-2.630.24791420.22441878X-RAY DIFFRACTION100
2.63-2.680.27561440.2131915X-RAY DIFFRACTION99.85
2.68-2.740.27951300.21831899X-RAY DIFFRACTION100
2.74-2.80.26321380.19921914X-RAY DIFFRACTION100
2.8-2.860.28081360.19561911X-RAY DIFFRACTION100
2.86-2.930.27571420.21891902X-RAY DIFFRACTION100
2.93-3.010.25241370.20741914X-RAY DIFFRACTION100
3.01-3.10.23171440.19911938X-RAY DIFFRACTION100
3.1-3.20.23641420.21191902X-RAY DIFFRACTION100
3.2-3.310.25821380.21411880X-RAY DIFFRACTION100
3.32-3.450.27791400.20771948X-RAY DIFFRACTION100
3.45-3.60.21121330.2111897X-RAY DIFFRACTION100
3.6-3.790.3727900.33551228X-RAY DIFFRACTION64.45
3.79-4.030.26681440.23951737X-RAY DIFFRACTION91.44
4.03-4.340.22531300.17781925X-RAY DIFFRACTION100
4.34-4.780.25341360.15891927X-RAY DIFFRACTION100
4.78-5.460.23841380.17881899X-RAY DIFFRACTION100
5.46-6.870.21851370.21661901X-RAY DIFFRACTION100
6.87-28.960.18531380.17871897X-RAY DIFFRACTION98.98

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