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- PDB-5ket: Structure of the aldo-keto reductase from Coptotermes gestroi -

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Basic information

Entry
Database: PDB / ID: 5ket
TitleStructure of the aldo-keto reductase from Coptotermes gestroi
ComponentsAldo-keto reductase 1
KeywordsOXIDOREDUCTASE / aldo-keto reductase / Coptotermes gestroi / celulose degradation / NADP
Function / homology
Function and homology information


D-threo-aldose 1-dehydrogenase activity / nucleotide binding
Similarity search - Function
Aldo/keto reductase family putative active site signature. / 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 putative active site signature. / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase 1
Similarity search - Component
Biological speciesCoptotermes gestroi (cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsLiberato, M.L. / Campos, B.M. / Tramontina, R. / Squina, F.M.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/04105-4 Brazil
Sao Paulo Research Foundation (FAPESP)2014/50371-8 Brazil
Sao Paulo Research Foundation (FAPESP)2014/20576-7 Brazil
Sao Paulo Research Foundation (FAPESP)2013/06336-0 Brazil
CitationJournal: Biotechnol Biofuels / Year: 2017
Title: The Coptotermes gestroi aldo-keto reductase: a multipurpose enzyme for biorefinery applications.
Authors: Tramontina, R. / Franco Cairo, J.P. / Liberato, M.V. / Mandelli, F. / Sousa, A. / Santos, S. / Rabelo, S.C. / Campos, B. / Ienczak, J. / Ruller, R. / Damasio, A.R. / Squina, F.M.
History
DepositionJun 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Refinement description / Category: citation / software
Item: _citation.country / _citation.journal_id_ISSN / _software.classification
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 31, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: 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: Aldo-keto reductase 1
B: Aldo-keto reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1834
Polymers76,6962
Non-polymers1,4872
Water0
1
A: Aldo-keto reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0912
Polymers38,3481
Non-polymers7431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aldo-keto reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0912
Polymers38,3481
Non-polymers7431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.141, 131.141, 290.657
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Aldo-keto reductase 1 /


Mass: 38347.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coptotermes gestroi (cockroach) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A140CVV2
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3

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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: 3.25 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M magnesium sulfate, 10% PEG400, 2 M ammonium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.46 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.46 Å / Relative weight: 1
ReflectionResolution: 2.85→44.74 Å / Num. obs: 22740 / % possible obs: 99.8 % / Redundancy: 8.6 % / Biso Wilson estimate: 48.8 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.29 / Rpim(I) all: 0.105 / Rrim(I) all: 0.309 / Net I/σ(I): 8.6 / Num. measured all: 195360
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.85-37.51.6482439832590.5360.6431.7721.599.9
9.01-44.7480.04661277690.9990.0170.0493397.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.41 Å44.74 Å
Translation5.41 Å44.74 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.8data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.2data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HBK

4hbk


Resolution: 2.85→44.744 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.293 1121 5.05 %
Rwork0.2389 21075 -
obs0.2417 22196 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.39 Å2 / Biso mean: 50.8213 Å2 / Biso min: 19.27 Å2
Refinement stepCycle: final / Resolution: 2.85→44.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4950 0 96 0 5046
Biso mean--71.76 --
Num. residues----642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095165
X-RAY DIFFRACTIONf_angle_d0.9687054
X-RAY DIFFRACTIONf_chiral_restr0.05801
X-RAY DIFFRACTIONf_plane_restr0.006908
X-RAY DIFFRACTIONf_dihedral_angle_d13.7753045
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8501-2.97980.41311390.335126572796100
2.9798-3.13690.40281430.325126562799100
3.1369-3.33330.34561390.30512655279499
3.3333-3.59060.35751630.28462590275397
3.5906-3.95170.31561290.25742450257991
3.9517-4.52310.2521390.18592703284299
4.5231-5.69680.22351360.1912690282698
5.6968-44.7490.21891330.19932674280794
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)
14.4849-0.19331.31623.0792-0.4823.4480.50740.4299-0.0925-0.2032-0.17040.08870.61910.15-0.31170.350.0506-0.04940.260.02460.3436-50.125797.707237.7175
24.97751.3178-0.773.2957-0.46523.5269-0.01880.49021.7931-0.99580.14610.6186-0.3699-0.4307-0.26210.38760.04670.13370.44420.25080.4981-40.6188118.617233.4741
32.3996-0.44341.7550.9912-0.20022.07890.3154-0.0272-0.00570.0963-0.0207-0.0210.5325-0.1078-0.25220.40530.023-0.04690.17620.01870.3344-40.155497.904649.8009
43.0971-0.58440.80454.41740.16272.84350.29560.03050.21330.2238-0.21920.077-0.19840.4569-0.07380.3101-0.02910.00880.2303-0.0050.4267-32.1783107.273351.8853
52.8303-1.1119-0.13532.5331-1.45975.19860.0351-0.62880.35010.20530.0685-0.0023-0.4067-0.0021-0.10640.2576-0.03630.02470.3712-0.08670.3031-38.3714118.407288.3839
61.71340.87740.32256.43211.52340.92370.1713-0.2779-0.17920.3648-0.0056-0.3701-0.02-0.0843-0.16710.26610.0222-0.01590.42020.04210.3192-48.9847113.002690.0396
76.9986-1.26940.23212.2527-0.01140.8634-0.296-1.4382-1.16651.03850.33530.48-0.2306-0.4998-0.10260.5810.04940.00640.62380.15220.2797-50.125695.41393.6535
84.1523-0.33590.02856.66981.35254.9435-0.3043-0.0714-0.03340.43760.03441.3620.2851-0.87920.23010.2971-0.05910.04990.30740.06080.4769-54.5304109.047882.1936
93.1957-5.08541.28078.0936-1.36834.66250.13410.1870.3052-0.5513-0.17910.48260.567-0.1631-0.06640.3048-0.0586-0.02490.2579-0.02080.3454-50.6356105.318874.4479
107.12090.54070.04051.64750.29072.3461-0.20280.5815-0.33110.0991-0.17680.1734-0.34840.0480.370.20550.0029-0.02080.3225-0.05080.1955-37.2523105.146869.7277
115.87853.51820.11724.48993.41184.66270.5070.334-0.35080.44580.3027-0.56930.34530.4822-0.34820.2110.12420.0990.4489-0.06640.5213-34.1841106.888680.3873
124.0619-0.592-0.60183.9115-0.01863.9858-0.0759-0.23270.42890.09030.0229-0.24930.2150.51210.01020.17210.02230.01490.3783-0.03280.2185-24.497110.0877.1589
131.6192-1.1786-0.69540.78510.56752.3052-0.2921-0.21760.1315-0.0867-0.3211-0.6061-0.08790.17420.54610.2459-0.05350.0480.458-0.1090.606-24.8784120.009779.2567
142.22910.15630.94790.3516-0.50321.57990.2139-0.0621-0.4155-0.2122-0.0006-0.08860.51540.4178-0.24420.49630.08320.05460.2336-0.03720.4928-35.069397.843674.1886
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 118 )A7 - 118
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 143 )A119 - 143
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 297 )A144 - 297
4X-RAY DIFFRACTION4chain 'A' and (resid 298 through 334 )A298 - 334
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 67 )B3 - 67
6X-RAY DIFFRACTION6chain 'B' and (resid 68 through 118 )B68 - 118
7X-RAY DIFFRACTION7chain 'B' and (resid 119 through 143 )B119 - 143
8X-RAY DIFFRACTION8chain 'B' and (resid 144 through 169 )B144 - 169
9X-RAY DIFFRACTION9chain 'B' and (resid 170 through 190 )B170 - 190
10X-RAY DIFFRACTION10chain 'B' and (resid 191 through 207 )B191 - 207
11X-RAY DIFFRACTION11chain 'B' and (resid 208 through 224 )B208 - 224
12X-RAY DIFFRACTION12chain 'B' and (resid 225 through 279 )B225 - 279
13X-RAY DIFFRACTION13chain 'B' and (resid 280 through 295 )B280 - 295
14X-RAY DIFFRACTION14chain 'B' and (resid 296 through 334 )B296 - 334

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