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- PDB-3uf0: Crystal structure of a putative NAD(P) dependent gluconate 5-dehy... -

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Basic information

Entry
Database: PDB / ID: 3uf0
TitleCrystal structure of a putative NAD(P) dependent gluconate 5-dehydrogenase from Beutenbergia cavernae(EFI target EFI-502044) with bound NADP (low occupancy)
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / gluconate / gluconate 5-dehydratase / NAD(P) dependent / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


2-deoxy-D-gluconate 3-dehydrogenase / 2-deoxy-D-gluconate 3-dehydrogenase activity / nucleotide binding
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Short-chain dehydrogenase/reductase SDR
Similarity search - Component
Biological speciesBeutenbergia cavernae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Hillerich, B. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Hillerich, B. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of a putative NAD(P) dependent gluconate 5-dehydrogenase from Beutenbergia cavernae(EFI target EFI-502044) with bound NADP (low occupancy)
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Hillerich, B. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Hillerich, B. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionOct 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5274
Polymers56,0412
Non-polymers1,4872
Water3,279182
1
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,0558
Polymers112,0814
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area17480 Å2
ΔGint-75 kcal/mol
Surface area29920 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-22 kcal/mol
Surface area18190 Å2
MethodPISA
3
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,0558
Polymers112,0814
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5030 Å2
ΔGint-27 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.470, 115.470, 76.182
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-321-

HOH

Detailsbiological unit is an tetramer

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Components

#1: Protein Short-chain dehydrogenase/reductase SDR


Mass: 28020.342 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beutenbergia cavernae (bacteria) / Strain: DSM 12333 / Gene: Bcav_0642 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C5BY10, 2-deoxy-D-gluconate 3-dehydrogenase
#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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffuction / pH: 4.6
Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM DTT, 5 mM MgCl2; Reservoir (100 mM NaAcetate pH 4.6, 2 M NaFormate); Cryoprotection (Reservoir + 20% glycerol), sitting drop ...Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM DTT, 5 mM MgCl2; Reservoir (100 mM NaAcetate pH 4.6, 2 M NaFormate); Cryoprotection (Reservoir + 20% glycerol), sitting drop vapor diffuction, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2011 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→81.685 Å / Num. all: 35340 / Num. obs: 35340 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rsym value: 0.071 / Net I/σ(I): 20.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.1110.50.4241.85302950480.42499.9
2.11-2.2410.60.2762.85103748130.276100
2.24-2.3910.70.1923.94839445270.19299.9
2.39-2.5810.70.1435.14548842320.143100
2.58-2.8310.90.17.34248939150.1100
2.83-3.1611.20.0729.73986835540.072100
3.16-3.6511.30.0659.53573731630.065100
3.65-4.4710.70.05611.22896727100.056100
4.47-6.3212.20.04114.42590321310.041100
6.32-42.7410.90.03318.81356712470.03398.8

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3o03

3o03


Resolution: 2→42.745 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.8781 / SU ML: 0.22 / σ(F): 0 / σ(I): 0 / Phase error: 18.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1946 1712 5 %RANDOM
Rwork0.1616 ---
all0.1633 34249 --
obs0.1633 34249 96.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.733 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso max: 110.49 Å2 / Biso mean: 36.6866 Å2 / Biso min: 11 Å2
Baniso -1Baniso -2Baniso -3
1--1.3279 Å2-0 Å20 Å2
2---1.3279 Å20 Å2
3---2.6559 Å2
Refinement stepCycle: LAST / Resolution: 2→42.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 96 182 3834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073803
X-RAY DIFFRACTIONf_angle_d1.0345208
X-RAY DIFFRACTIONf_chiral_restr0.095597
X-RAY DIFFRACTIONf_plane_restr0.004678
X-RAY DIFFRACTIONf_dihedral_angle_d17.7251296
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9993-2.05810.21511320.17162486261891
2.0581-2.12450.24191210.16462602272394
2.1245-2.20050.22251310.15712588271994
2.2005-2.28860.20621250.15692620274594
2.2886-2.39270.22811460.16442665281196
2.3927-2.51890.28221350.17682689282497
2.5189-2.67660.21361480.17552705285398
2.6766-2.88330.20311240.17422780290499
2.8833-3.17330.21211520.17622771292399
3.1733-3.63230.18521680.166728022970100
3.6323-4.57550.1531660.142528282994100
4.5755-42.75480.18731640.156130013165100
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)
10.2407-0.07870.24090.55390.00590.4622-0.01760.1394-0.00580.00590.0335-0.38530.15920.4201-0.02660.21510.08090.0650.2911-0.03340.295639.9518-0.061928.9669
20.25980.4576-0.02810.85630.1550.83780.1768-0.08920.1958-0.12320.0175-0.49580.0970.38640.12630.2720.08850.16580.4297-0.00240.374745.11920.064820.7913
31.92470.79350.15840.74710.55010.57350.21570.2419-0.3166-0.6926-0.0365-0.1751-0.3869-0.1356-0.07030.44620.090.03850.2458-0.0550.27430.5357-3.983413.6425
40.453-0.26810.05170.23620.13570.35820.05520.16640.2339-0.10080.0275-0.2745-0.19670.2437-0.04780.3717-0.00480.06080.2673-0.00320.375832.02879.147321.7896
50.8252-0.37740.04630.39410.14390.59880.14130.2054-0.1883-0.1839-0.07160.02410.10670.1961-0.01930.27380.00710.06160.228-0.03520.221325.98696.262618.4995
60.5855-0.3-0.02650.15840.07910.66350.0065-0.02050.10850.11220.0112-0.0498-0.21090.072-0.01150.1971-0.0250.02320.1708-0.00910.225123.90510.182628.4581
70.15420.11670.15830.3250.140.3468-0.06930.0225-0.0341-0.07010.0741-0.1939-0.0030.21450.02860.1536-0.02280.03090.2239-0.01190.230235.030915.28436.002
80.09210.1763-0.06870.62840.19740.51410.1570.28790.0325-0.472-0.1080.2984-0.0479-0.2230.04270.47130.1275-0.13290.35820.04750.18342.718429.745312.2227
90.4414-0.33330.08940.27750.04670.40530.06590.1348-0.0521-0.1450.01950.1709-0.0202-0.06880.00340.2034-0.0108-0.00250.1080.02170.123414.783720.998719.9096
100.6083-0.3284-0.05150.17890.00190.94370.06940.0988-0.0633-0.1624-0.03880.1321-0.0068-0.1944-0.01290.20540.0057-0.05060.19-0.02560.20762.81418.846329.9624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 26:64)A26 - 64
2X-RAY DIFFRACTION2chain 'A' and (resseq 65:90)A65 - 90
3X-RAY DIFFRACTION3chain 'A' and (resseq 91:104)A91 - 104
4X-RAY DIFFRACTION4chain 'A' and (resseq 105:126)A105 - 126
5X-RAY DIFFRACTION5chain 'A' and (resseq 127:155)A127 - 155
6X-RAY DIFFRACTION6chain 'A' and (resseq 156:199)A156 - 199
7X-RAY DIFFRACTION7chain 'A' and (resseq 200:273)A200 - 273
8X-RAY DIFFRACTION8chain 'B' and (resseq 26:104)B26 - 104
9X-RAY DIFFRACTION9chain 'B' and (resseq 105:199)B105 - 199
10X-RAY DIFFRACTION10chain 'B' and (resseq 200:273)B200 - 273

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