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- PDB-4ejm: Crystal structure of a putative zinc-binding dehydrogenase (Targe... -

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Basic information

Entry
Database: PDB / ID: 4ejm
TitleCrystal structure of a putative zinc-binding dehydrogenase (Target PSI-012003) from Sinorhizobium meliloti 1021 bound to NADP
ComponentsPutative zinc-binding dehydrogenase
KeywordsOXIDOREDUCTASE / NADP / Structural genomics / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / nucleotide binding / zinc ion binding
Similarity search - Function
: / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal ...: / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Zinc-binding dehydrogenase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.09 Å
AuthorsSampathkumar, P. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a putative zinc-binding dehydrogenase (target nysgrc-012003) from sinorhizobium meliloti 1021 bound to NADP
Authors: Sampathkumar, P. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Gizzi, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / Love, J.D. / ...Authors: Sampathkumar, P. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Gizzi, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / Love, J.D. / Matikainen, B. / Patskovsky, Y. / Seidel, R. / Toro, R. / Zencheck, W. / Almo, S.C.
History
DepositionApr 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative zinc-binding dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0126
Polymers39,0171
Non-polymers9955
Water1,982110
1
A: Putative zinc-binding dehydrogenase
hetero molecules

A: Putative zinc-binding dehydrogenase
hetero molecules

A: Putative zinc-binding dehydrogenase
hetero molecules

A: Putative zinc-binding dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,04924
Polymers156,0694
Non-polymers3,98020
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_555x,-y,-z1
Buried area19160 Å2
ΔGint-38 kcal/mol
Surface area47130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.620, 107.620, 137.741
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-525-

HOH

DetailsThe biological assembly is a probable tetramer

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Components

#1: Protein Putative zinc-binding dehydrogenase / short-chain dehydrogenase


Mass: 39017.254 Da / Num. of mol.: 1 / Mutation: R72V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: R01577, SMc01214 / Plasmid: pSGC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q92PZ3, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 298 K / pH: 6.2
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (MCSG2 #1: 0.2 M Potassium Sodium Tartarate and 20% (w/v) PEG3350 ); Cryoprotection (30% Ethylene glycol); Crystals soaked ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (MCSG2 #1: 0.2 M Potassium Sodium Tartarate and 20% (w/v) PEG3350 ); Cryoprotection (30% Ethylene glycol); Crystals soaked in 100mM NADP and 100mM 3-hydroxybutyrate-Na in 15% PEG3350 and 30% ethyleneglycol for at least 30mins, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 26, 2011 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 24190 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Biso Wilson estimate: 35 Å2 / Rsym value: 0.118 / Net I/σ(I): 22.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.08 / Rsym value: 0.917 / % possible all: 91.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementResolution: 2.09→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.149 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1229 5.1 %RANDOM
Rwork0.185 ---
obs0.186 24174 98.8 %-
all-24190 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.09→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 0 61 110 2657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192618
X-RAY DIFFRACTIONr_bond_other_d0.0010.021768
X-RAY DIFFRACTIONr_angle_refined_deg1.5462.0153573
X-RAY DIFFRACTIONr_angle_other_deg0.93734331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3495351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95423.01193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.49315408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7811524
X-RAY DIFFRACTIONr_chiral_restr0.0840.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212912
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02497
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.08→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 78 -
Rwork0.231 1399 -
obs--87.71 %

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