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- PDB-6grl: Structure of imine reductase (apo form) at 1.6 A resolution from ... -

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Basic information

Entry
Database: PDB / ID: 6grl
TitleStructure of imine reductase (apo form) at 1.6 A resolution from Saccharomonospora xinjiangensis
ComponentsBeta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / Imine Reductase / S-selective / Reductive Amination
Function / homology
Function and homology information


NADP binding / oxidoreductase activity
Similarity search - Function
3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase
Similarity search - Component
Biological speciesSaccharomonospora xinjiangensis XJ-54 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHasan, M. / Gand, M. / Logan, D.T. / Hoehne, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
European UnionECOST-STSM-CM1303-040515-058745 Germany
CitationJournal: To Be Published
Title: Structure of imine reductase (apo form) at 1.6 A resolution from Saccharomonospora xinjiangensis
Authors: Hasan, M. / Gand, M. / Logan, D.T. / Hoehne, M.
History
DepositionJun 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Beta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)32,1391
Polymers32,1391
Non-polymers00
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.184, 35.774, 53.050
Angle α, β, γ (deg.)90.00, 91.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase


Mass: 32139.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomonospora xinjiangensis XJ-54 (bacteria)
Gene: SacxiDRAFT_0617 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I0UYD6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M imidazole malate 7.0 and 25 % PEG w/v 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.6→43.09 Å / Num. obs: 33393 / % possible obs: 94.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 16.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.02 / Rrim(I) all: 0.039 / Net I/av σ(I): 26.09 / Net I/σ(I): 26.09
Reflection shellResolution: 1.6→1.6473 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZGY

3zgy


Resolution: 1.6→41.712 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3
RfactorNum. reflection% reflection
Rfree0.2159 1684 5.05 %
Rwork0.193 --
obs0.1942 33328 94.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→41.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2110 0 0 263 2373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022221
X-RAY DIFFRACTIONf_angle_d0.4663029
X-RAY DIFFRACTIONf_dihedral_angle_d9.6541794
X-RAY DIFFRACTIONf_chiral_restr0.038349
X-RAY DIFFRACTIONf_plane_restr0.004403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6002-1.64730.21311300.18062561X-RAY DIFFRACTION92
1.6473-1.70040.19841360.19212664X-RAY DIFFRACTION96
1.7004-1.76120.28141430.21442674X-RAY DIFFRACTION97
1.7612-1.83170.23631310.21672718X-RAY DIFFRACTION98
1.8317-1.91510.27661220.2312516X-RAY DIFFRACTION90
1.9151-2.01610.24721350.21322505X-RAY DIFFRACTION90
2.0161-2.14240.20161290.21022556X-RAY DIFFRACTION91
2.1424-2.30780.20121170.20332493X-RAY DIFFRACTION89
2.3078-2.540.22151750.19852736X-RAY DIFFRACTION98
2.54-2.90740.20451510.20082726X-RAY DIFFRACTION97
2.9074-3.66270.20741890.1872701X-RAY DIFFRACTION97
3.6627-41.72580.20681260.16492794X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.06950.7715-0.12191.4481-0.56741.2490.0539-0.25010.45370.23690.04440.1165-0.76530.17560.60130.2267-0.01950.03940.0057-0.0070.0518-32.592123.495416.0186
22.0287-0.28031.32362.38040.28120.9861-0.0622-0.40360.25410.26490.11030.1254-0.3034-0.39430.06040.26950.04210.04630.1033-0.02620.1374-38.48821.371418.9214
30.5531-0.0833-0.13390.4757-0.71181.1985-0.12480.0056-0.34690.10690.09790.16260.5513-0.4807-0.3310.2233-0.0220.037-0.02240.01150.0992-36.128112.873712.1755
40.8132-0.02340.30730.53420.1222.41870.0212-0.0181-0.08710.0052-0.0544-0.02370.21070.1281-0.0620.149-0.0053-0.0070.0281-0.00910.0913-31.482611.80037.2235
53.03530.00171.51522.24530.52163.42780.104-0.0412-0.2675-0.06880.0518-0.14370.15360.2664-0.11380.110.00830.00940.0791-0.00050.1168-24.60888.24155.6928
60.1571-0.17790.48920.2997-0.34892.29810.1651-0.30070.08160.2948-0.082-0.21030.22640.2633-0.42880.1779-0.1135-0.04390.2304-0.05210.1463-19.620420.886417.8616
71.657-1.47041.07226.29540.49551.15810.13160.25210.2261-0.7593-0.1582-0.2539-0.31970.5065-0.17990.1545-0.07240.00030.1390.03260.1571-19.170620.95226.555
81.89530.34982.15120.47580.2992.3894-0.0108-0.31730.12010.0159-0.1347-0.0368-0.1976-0.23680.1890.0738-0.021-0.02570.2907-0.03210.186-2.89459.387531.6669
91.5281-0.7177-0.27892.14120.97930.45920.01560.62970.5042-0.4133-0.1185-0.3332-0.33390.3893-0.12840.211-0.02130.0030.50250.15490.34298.886812.61615.308
102.32590.84080.05650.97350.18960.10550.17470.371-0.1749-0.1371-0.144-0.23430.27980.3361-0.09930.12850.05960.01290.39390.06750.289111.1908-0.562223.4207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 34 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 89 )
4X-RAY DIFFRACTION4chain 'A' and (resid 90 through 106 )
5X-RAY DIFFRACTION5chain 'A' and (resid 107 through 130 )
6X-RAY DIFFRACTION6chain 'A' and (resid 131 through 148 )
7X-RAY DIFFRACTION7chain 'A' and (resid 149 through 173 )
8X-RAY DIFFRACTION8chain 'A' and (resid 174 through 220 )
9X-RAY DIFFRACTION9chain 'A' and (resid 221 through 243 )
10X-RAY DIFFRACTION10chain 'A' and (resid 244 through 296 )

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