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- PDB-4id9: Crystal structure of a short-chain dehydrogenase/reductase superf... -

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Basic information

Entry
Database: PDB / ID: 4id9
TitleCrystal structure of a short-chain dehydrogenase/reductase superfamily protein from agrobacterium tumefaciens (TARGET EFI-506441) with bound nad, monoclinic form 1
ComponentsSHORT-CHAIN DEHYDROGENASE/REDUCTASEShort-chain dehydrogenase
KeywordsOXIDOREDUCTASE / putative dehydrogenase / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


UDP-galactose 4-epimerase; domain 1 - #60 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ALANINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsVetting, M.W. / 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 short-chain dehydrogenase/reductase superfamily protein from agrobacterium tumefaciens (TARGET EFI-506441) with bound nad, monoclinic form 1
Authors: Vetting, M.W. / Groninger-Poe, F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionDec 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 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_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
B: SHORT-CHAIN DEHYDROGENASE/REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6557
Polymers76,1682
Non-polymers1,4875
Water14,898827
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-37 kcal/mol
Surface area26530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.356, 74.426, 95.341
Angle α, β, γ (deg.)90.000, 97.100, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is a dimer

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Components

#1: Protein SHORT-CHAIN DEHYDROGENASE/REDUCTASE / Short-chain dehydrogenase


Mass: 38083.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (bacteria) / Strain: str. C58 / Gene: galE, Atu5463 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CL58
#2: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 827 / 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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 6.5
Details: Protein (10mM Tris pH 7.9, 5 mM NAD, 5 mM UDP-GAL; Reservoir (0.2 M Ammonium Acetate, 0.1 M Bis-Tris:HCl pH 6.5, 25% (w/v) PEG 3350); Cryoprotection (0.40 mM Ammonium Acetate, 0.20 mM Bis- ...Details: Protein (10mM Tris pH 7.9, 5 mM NAD, 5 mM UDP-GAL; Reservoir (0.2 M Ammonium Acetate, 0.1 M Bis-Tris:HCl pH 6.5, 25% (w/v) PEG 3350); Cryoprotection (0.40 mM Ammonium Acetate, 0.20 mM Bis-Tris:HCl pH 6.5, 40% (w/v) PEG 3350, 5 mM NAD, 5 mM UDP-GAL), sitting drop vapor diffusion, 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: Dec 8, 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: 1.6→94.61 Å / Num. obs: 94951 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4695 / % possible all: 98.8

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Processing

Software
NameVersionClassificationNB
SCALA0.1.27data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ENK

3enk


Resolution: 1.6→29.248 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.8457 / SU ML: 0.18 / σ(F): 0 / σ(I): 0 / Phase error: 22.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 4747 5.01 %RANDOM
Rwork0.181 ---
all0.1825 94727 --
obs0.1825 94727 98.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.23 Å2 / Biso mean: 21.805 Å2 / Biso min: 6.76 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5007 0 95 827 5929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065347
X-RAY DIFFRACTIONf_angle_d1.0787276
X-RAY DIFFRACTIONf_chiral_restr0.074789
X-RAY DIFFRACTIONf_plane_restr0.005979
X-RAY DIFFRACTIONf_dihedral_angle_d13.9881990
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.61820.29151790.26052984316399
1.6182-1.63720.26991690.25152983315299
1.6372-1.65720.27311340.23163007314199
1.6572-1.67820.24361670.23042983315099
1.6782-1.70020.25871620.22832992315499
1.7002-1.72350.25991540.21142980313499
1.7235-1.74820.27091440.219930693213100
1.7482-1.77420.28761620.22162948311099
1.7742-1.8020.25091640.21043016318099
1.802-1.83150.26951450.208229983143100
1.8315-1.86310.27181590.214930573216100
1.8631-1.89690.24461750.21282955313099
1.8969-1.93340.30561580.21443006316499
1.9334-1.97290.24111460.21583016316299
1.9729-2.01580.23431520.208630363188100
2.0158-2.06270.25911520.192729833135100
2.0627-2.11420.2231900.19292996318699
2.1142-2.17140.251550.1930223177100
2.1714-2.23520.22371610.18372986314799
2.2352-2.30740.23081700.19042974314499
2.3074-2.38980.19741540.18293056321099
2.3898-2.48540.22131630.18092959312299
2.4854-2.59850.21341570.17882997315499
2.5985-2.73540.20171510.17953017316898
2.7354-2.90660.22991500.18422978312898
2.9066-3.13080.22261470.17622978312598
3.1308-3.44540.18861600.16082970313098
3.4454-3.94290.1651480.15063016316498
3.9429-4.96380.14551600.13753009316998
4.9638-29.25260.17091590.16513009316896
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)
10.2088-0.10660.00560.22030.09120.3715-0.0201-0.03840.07150.0412-0.0081-0.0397-0.12560.044800.08890.0021-0.00870.1149-0.00990.1259.401850.407985.8846
20.3130.11510.16080.18740.17520.6658-0.06630.009-0.0342-0.04830.004-0.01920.11110.0258-0.00240.10480.00930.00720.0583-0.00210.067250.777937.588876.5704
30.57590.1399-0.43260.0277-0.06360.8154-0.005-0.0596-0.065-0.0296-0.0131-0.02240.12910.0259-0.00230.15410.02920.00820.08790.02660.080946.110333.255196.6993
428.962222-8.30932.0001-0.15690.0234-0.98520.98930.65340.78730.7056-0.4316-0.53450.3862-0.00840.06930.0498-0.08270.251947.377147.4821118.2346
50.1697-0.05290.07210.3352-0.07630.2784-0.02970.01440.0902-0.0741-0.07150.0434-0.0609-0.006-0.00890.0982-0.0211-0.01920.1112-0.00240.139333.258245.895353.2846
60.145-0.04390.22750.09990.20760.5878-0.0766-0.0266-0.02870.07450.03110.00170.10160.025-0.00010.1266-0.01030.00490.08240.00280.086944.798536.612762.4971
70.47010.0438-0.27970.18640.02850.7279-0.01640.0618-0.01840.0616-0.0044-0.0260.063-0.00950.01390.0746-0.0187-0.0060.0572-0.00710.094351.450232.905343.672
80.04260.0118-0.03950.01010.02510.1102-0.04970.02260.0664-0.15450.13690.16370.1039-0.1452-00.1753-0.0426-0.00270.1797-0.00580.104545.602739.169926.1327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:71 )A1 - 71
2X-RAY DIFFRACTION2( CHAIN A AND RESID 72:149 )A72 - 149
3X-RAY DIFFRACTION3( CHAIN A AND RESID 150:321 )A150 - 321
4X-RAY DIFFRACTION4( CHAIN A AND RESID 401:401 )A401
5X-RAY DIFFRACTION5( CHAIN B AND RESID 0:71 )B0 - 71
6X-RAY DIFFRACTION6( CHAIN B AND RESID 72:149 )B72 - 149
7X-RAY DIFFRACTION7( CHAIN B AND RESID 150:305 )B150 - 305
8X-RAY DIFFRACTION8( CHAIN B AND RESID 306:327 )B306 - 327

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