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- PDB-4hp8: Crystal structure of a putative 2-deoxy-d-gluconate 3-dehydrogena... -

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Basic information

Entry
Database: PDB / ID: 4hp8
TitleCrystal structure of a putative 2-deoxy-d-gluconate 3-dehydrogenase from Agrobacterium Tumefaciens (target EFI-506435) with bound NADP
Components2-deoxy-D-gluconate 3-dehydrogenase
KeywordsOXIDOREDUCTASE / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


2-deoxy-D-gluconate 3-dehydrogenase activity / NAD binding
Similarity search - Function
2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase / 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
ACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2-deoxy-D-gluconate 3-dehydrogenase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsVetting, M.W. / Bouvier, J.T. / Groninger-Poe, F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of a putative 2-deoxy-d-gluconate 3-dehydrogenase from Agrobacterium Tumefaciens (target EFI-506435) with bound NADP
Authors: Vetting, M.W. / Bouvier, J.T. / Groninger-Poe, F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Gerlt, J.A. / Almo, S.C.
History
DepositionOct 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 2-deoxy-D-gluconate 3-dehydrogenase
B: 2-deoxy-D-gluconate 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0945
Polymers51,5482
Non-polymers1,5463
Water10,827601
1
A: 2-deoxy-D-gluconate 3-dehydrogenase
B: 2-deoxy-D-gluconate 3-dehydrogenase
hetero molecules

A: 2-deoxy-D-gluconate 3-dehydrogenase
B: 2-deoxy-D-gluconate 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,18810
Polymers103,0974
Non-polymers3,0926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area18090 Å2
ΔGint-86 kcal/mol
Surface area31510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.022, 93.022, 109.285
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

21A-602-

HOH

31B-492-

HOH

41B-581-

HOH

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Components

#1: Protein 2-deoxy-D-gluconate 3-dehydrogenase


Mass: 25774.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / ATCC 33970 / Gene: kduD, Atu3141 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CEQ9
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Protein (10mM Tris, pH 7.9), Reservoir (0.1 M Bis-Tris:HCl, pH 6.5, 2.0 M Ammonium Sulfate, 10 mM NADP), Cryoprotection (Reservoir + 20% Ethylene glycol), vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 18, 2012 / 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: 1.35→109.285 Å / Num. all: 105259 / Num. obs: 105259 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Rmerge(I) obs: 0.116 / Rsym value: 0.116 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.35-1.4214.40.7551218771151460.75599.8
1.42-1.5114.50.5251.4207687143590.52599.9
1.51-1.6114.50.3442.1195934135450.344100
1.61-1.7414.50.2443183202126110.244100
1.74-1.9114.60.1634.5170780116870.163100
1.91-2.1314.70.1185.6156040105820.118100
2.13-2.4614.80.1254.613874293810.125100
2.46-3.0214.80.0976.211829480180.097100
3.02-4.2714.60.04812.49172563010.048100
4.27-25.813.60.03516.44952536290.03599.4

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3UF0

3uf0


Resolution: 1.35→25.8 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.9262 / SU ML: 0.09 / σ(F): 0 / σ(I): 0 / Phase error: 13.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1562 5254 5 %RANDOM
Rwork0.1386 ---
all0.1395 105176 --
obs0.1395 105176 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.89 Å2 / Biso mean: 12.5098 Å2 / Biso min: 2.83 Å2
Refinement stepCycle: LAST / Resolution: 1.35→25.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3609 0 100 601 4310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153840
X-RAY DIFFRACTIONf_angle_d1.7225239
X-RAY DIFFRACTIONf_chiral_restr0.1598
X-RAY DIFFRACTIONf_plane_restr0.009681
X-RAY DIFFRACTIONf_dihedral_angle_d19.3021364
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.35-1.36530.20351590.190133113470
1.3653-1.38140.18631720.176632683440
1.3814-1.39820.18621860.172332533439
1.3982-1.41590.18791810.165332923473
1.4159-1.43460.16581620.15732933455
1.4346-1.45420.18471560.155432943450
1.4542-1.4750.17851790.155332933472
1.475-1.4970.18171890.149832753464
1.497-1.52040.16341740.132132703444
1.5204-1.54530.14361780.128933193497
1.5453-1.5720.16051730.130332863459
1.572-1.60060.16081560.128233213477
1.6006-1.63130.16111570.124333363493
1.6313-1.66460.15561880.12632723460
1.6646-1.70080.15541700.126932963466
1.7008-1.74040.13831900.120933183508
1.7404-1.78390.1351650.12633253490
1.7839-1.83210.14311620.128733163478
1.8321-1.8860.16031810.128333243505
1.886-1.94690.14891760.129433313507
1.9469-2.01640.14451800.128233133493
2.0164-2.09710.16561840.136233243508
2.0971-2.19250.14511710.126133613532
2.1925-2.3080.13641760.133833403516
2.308-2.45250.16971760.138433763552
2.4525-2.64170.15791880.138833413529
2.6417-2.90720.1581660.147434003566
2.9072-3.32720.16591780.143634093587
3.3272-4.1890.13581770.133434563633
4.189-25.80430.15722040.149936093813
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)
10.39410.16240.05770.1495-0.02730.17190.0219-0.0732-0.02820.0546-0.0187-0.04080.0020.024400.0512-0.0031-0.01430.05630.00160.06432.54811.410816.3028
20.2029-0.01820.22450.3248-0.04680.2434-0.017-0.03170.01820.02010.0004-0.0603-0.00240.0365-0.00070.0336-0.00510.00380.0482-0.00560.051929.752514.17596.0229
30.43440.1410.09690.1555-0.2111-0.0380.0179-0.08360.02370.04120.0078-0.003-0.01150.00060.00030.03840.00210.00410.0396-0.01190.03416.85086.13139.6729
40.2748-0.1324-0.0760.2919-0.26510.23240.0266-0.0549-0.0844-0.093-0.0886-0.09290.18780.0229-0.0140.1530.01440.01640.03530.00570.092713.351-23.94668.7572
50.406-0.06860.19780.35670.02290.08540.0295-0.0331-0.0867-0.0277-0.00560.03150.1533-0.0738-0.020.097-0.03220.00740.05570.00210.0613-2.7965-18.21015.347
60.3182-0.03790.01820.2189-0.10860.01330.00450.0079-0.0359-0.0211-0.00160.01040.0488-0.030100.0614-0.00930.00850.0406-0.00690.04054.5539-9.27141.7871
70.0384-0.0574-0.05190.0840.07840.04770.02890.02210.0153-0.1128-0.0411-0.03450.07380.0047-00.08230.00820.00480.0534-0.01950.061716.6465-9.3005-13.4347
80.20470.03710.10540.0725-0.030.04850.0040.004-0.00780.0044-0.0198-0.04060.0456-0.014900.05540.00010.00640.0386-0.00270.053914.3723-7.03644.851
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 3:53)A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 54:128)A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 129:247)A0
4X-RAY DIFFRACTION4CHAIN B AND (RESID 2:54)B0
5X-RAY DIFFRACTION5CHAIN B AND (RESID 55:128)B0
6X-RAY DIFFRACTION6CHAIN B AND (RESID 129:196)B0
7X-RAY DIFFRACTION7CHAIN B AND (RESID 197:214)B0
8X-RAY DIFFRACTION8CHAIN B AND (RESID 215:247)B0

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