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- PDB-6m7k: Structure of mouse RECON (AKR1C13) in complex with cyclic AMP-AMP... -

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Basic information

Entry
Database: PDB / ID: 6m7k
TitleStructure of mouse RECON (AKR1C13) in complex with cyclic AMP-AMP-GMP (cAAG)
Components
  • Aldo-keto reductase family 1 member C13
  • cyclic AMP-AMP-GMP
KeywordsOXIDOREDUCTASE / RECON / innate immunity / AKR1C13 / cyclic AMP-AMP-GMP
Function / homology
Function and homology information


: / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / xenobiotic metabolic process
Similarity search - Function
Aldo-keto reductase family 1 member C / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel ...Aldo-keto reductase family 1 member C / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
RNA / Aldo-keto reductase family 1 member C13
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsEaglesham, J.B. / Whiteley, A.T. / de Oliveira Mann, C.C. / Morehouse, B.R. / Nieminen, E.A. / King, D.S. / Lee, A.S.Y. / Mekalanos, J.J. / Kranzusch, P.J.
CitationJournal: Nature / Year: 2019
Title: Bacterial cGAS-like enzymes synthesize diverse nucleotide signals.
Authors: Whiteley, A.T. / Eaglesham, J.B. / de Oliveira Mann, C.C. / Morehouse, B.R. / Lowey, B. / Nieminen, E.A. / Danilchanka, O. / King, D.S. / Lee, A.S.Y. / Mekalanos, J.J. / Kranzusch, P.J.
History
DepositionAug 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldo-keto reductase family 1 member C13
B: cyclic AMP-AMP-GMP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9656
Polymers37,7172
Non-polymers2484
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint12 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.597, 57.070, 110.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aldo-keto reductase family 1 member C13 / RECON / AKR1C13


Mass: 36758.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Akr1c13 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8VC28, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: RNA chain cyclic AMP-AMP-GMP / cAAG


Mass: 958.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.0 M lithium chloride, 0.1 M sodium acetate, 30% PEG6000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 16, 2018
RadiationMonochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.1→46.02 Å / Num. obs: 130194 / % possible obs: 99.7 % / Redundancy: 9.1 % / CC1/2: 0.999 / Rpim(I) all: 0.029 / Net I/σ(I): 14
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6242 / CC1/2: 0.813 / Rsym value: 0.298 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5UXF

5uxf


Resolution: 1.1→46.02 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.48
RfactorNum. reflection% reflectionSelection details
Rfree0.1574 2000 1.54 %0.02
Rwork0.1428 ---
obs0.143 130100 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.1→46.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2560 67 16 537 3180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112806
X-RAY DIFFRACTIONf_angle_d1.4213834
X-RAY DIFFRACTIONf_dihedral_angle_d17.0861069
X-RAY DIFFRACTIONf_chiral_restr0.21421
X-RAY DIFFRACTIONf_plane_restr0.01486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.12750.2261390.19958881X-RAY DIFFRACTION98
1.1275-1.1580.19321410.1859018X-RAY DIFFRACTION99
1.158-1.19210.17861410.17569098X-RAY DIFFRACTION100
1.1921-1.23060.17471420.16189080X-RAY DIFFRACTION100
1.2306-1.27460.17221420.15959102X-RAY DIFFRACTION100
1.2746-1.32560.16691430.15569100X-RAY DIFFRACTION100
1.3256-1.38590.16321420.15249122X-RAY DIFFRACTION100
1.3859-1.4590.15951420.14449109X-RAY DIFFRACTION100
1.459-1.55040.15831430.1399134X-RAY DIFFRACTION100
1.5504-1.67010.1531420.13299160X-RAY DIFFRACTION100
1.6701-1.83820.15891440.13359181X-RAY DIFFRACTION100
1.8382-2.10420.13631440.1259226X-RAY DIFFRACTION100
2.1042-2.65110.14121450.12859287X-RAY DIFFRACTION100
2.6511-46.06270.15521500.14179602X-RAY DIFFRACTION100
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)
11.2139-0.0167-0.58030.37650.11010.5947-0.0226-0.0157-0.05550.01250.02140.03360.015-0.09010.00570.0662-0.00560.00360.05890.00710.0653-20.8537-8.851918.2049
20.99320.37690.54940.64310.36690.65970.0116-0.0434-0.06860.0886-0.0013-0.01720.09040.0134-0.01960.07780.01220.00780.06090.00840.0699-4.2867-12.31921.9878
30.3714-0.1701-0.05330.55580.07610.3306-0.00020.0071-0.0098-0.028-0.00180.0079-0.00420.00310.00290.0555-0.00270.0010.05410.00260.0468-12.1365.182811.9279
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 143 )
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 323 )

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