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- PDB-2wzm: Crystal structure of a mycobacterium aldo-keto reductase in its a... -

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Basic information

Entry
Database: PDB / ID: 2wzm
TitleCrystal structure of a mycobacterium aldo-keto reductase in its apo and liganded form
ComponentsALDO-KETO REDUCTASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


: / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
Similarity search - Function
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
Chem-NA7 / Aldo-keto reductase MSMEG_2407/MSMEI_2346
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.64 Å
AuthorsScoble, J. / McAlister, A.D. / Fulton, Z. / Troy, S. / Byres, E. / Vivian, J.P. / Brammananth, R. / Wilce, M.C.J. / Le Nours, J. / Zaker-Tabrizi, L. ...Scoble, J. / McAlister, A.D. / Fulton, Z. / Troy, S. / Byres, E. / Vivian, J.P. / Brammananth, R. / Wilce, M.C.J. / Le Nours, J. / Zaker-Tabrizi, L. / Coppel, R.L. / Crellin, P.K. / Rossjohn, J. / Beddoe, T.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal Structure and Comparative Functional Analyses of a Mycobacterium Aldo-Keto Reductase.
Authors: Scoble, J. / Mcalister, A.D. / Fulton, Z. / Troy, S. / Byres, E. / Vivian, J.P. / Brammananth, R. / Wilce, M.C.J. / Le Nours, J. / Zaker-Tabrizi, L. / Coppel, R.L. / Crellin, P.K. / Rossjohn, J. / Beddoe, T.
History
DepositionNov 30, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALDO-KETO REDUCTASE
B: ALDO-KETO REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1934
Polymers59,9472
Non-polymers1,2472
Water9,422523
1
A: ALDO-KETO REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5972
Polymers29,9731
Non-polymers6231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALDO-KETO REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5972
Polymers29,9731
Non-polymers6231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.456, 65.456, 96.844
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein ALDO-KETO REDUCTASE / UNCHARACTERIZED OXIDOREDUCTASE MSMEG_2407


Mass: 29973.307 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2 155 / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QV09, EC: 1.1.1.218
#2: Chemical ChemComp-NA7 / [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4S)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE


Mass: 623.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N5O16P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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 Å3/Da / Density % sol: 38.4 % / Description: NONE
Crystal growpH: 7.6 / Details: 0.1M TRIS-HCL PH 7.6, 1.85 (NH4)2HPO4

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95367
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95367 Å / Relative weight: 1
ReflectionResolution: 1.64→36.8 Å / Num. obs: 57130 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.3
Reflection shellResolution: 1.64→1.71 Å / Redundancy: 5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.5 / % possible all: 85.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.64→56.7 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.082 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FIRST 9 RESIDUES WERE NOT MODELLED IN STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.22134 2895 5.1 %RANDOM
Rwork0.17808 ---
obs0.18029 54193 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.24 Å20 Å2
2--0.49 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.64→56.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4102 0 78 523 4703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224280
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.9865864
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3315552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01324.332187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61315635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5791530
X-RAY DIFFRACTIONr_chiral_restr0.090.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023260
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.22026
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22961
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2346
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7691.52783
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.28724356
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.01631700
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8434.51505
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: 1.635→1.678 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 191 -
Rwork0.274 3859 -
obs--94.89 %

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