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- PDB-4zgw: Short-chain dehydrogenase/reductase from Serratia marcescens BCRC... -

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Basic information

Entry
Database: PDB / ID: 4zgw
TitleShort-chain dehydrogenase/reductase from Serratia marcescens BCRC 10948
Componentsshort-chain dehydrogenase/reductase
KeywordsOXIDOREDUCTASE / short-chain dehydrogenase/reductase Serratia marcescens
Function / homologyEnoyl-(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 / Putative oxidoreductase
Function and homology information
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsWang, W.-C.
CitationJournal: To Be Published
Title: Stereoselective synthesis of (R)-phenylephrine using recombinant Escherichia coli cells expressing a novel short-chain dehydrogenase/reductase gene from Serratia marcescens BCRC 10948
Authors: Hsu, W.H.
History
DepositionApr 24, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: short-chain dehydrogenase/reductase
B: short-chain dehydrogenase/reductase


Theoretical massNumber of molelcules
Total (without water)59,3072
Polymers59,3072
Non-polymers00
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-10 kcal/mol
Surface area18230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.871, 83.871, 115.057
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-431-

HOH

21B-424-

HOH

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Components

#1: Protein short-chain dehydrogenase/reductase


Mass: 29653.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Strain: BCRC 10948 / Production host: ESCHERICHIA COLI BL21 (bacteria) / Strain (production host): BL21
References: UniProt: V5YUZ7*PLUS, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE N-TERMINAL AMINO ACIDS 1-39 ARE SEGEMENTS ON THE PET30A PLASMID.

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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: 1.71 Å3/Da / Density % sol: 27.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.8 M sodium formate, 0.1 M sodium cacodylate, 25% w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→20 Å / Num. obs: 69956 / % possible obs: 99.8 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 36.66
Reflection shellResolution: 1.47→1.52 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 4.44 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
Blu-Icedata collection
HKL-2000data processing
SCALEPACKdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V2G

3v2g


Resolution: 1.47→19.889 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.025 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19125 3392 5 %RANDOM
Rwork0.16618 ---
obs0.1674 65062 97.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.231 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.47→19.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 0 0 298 3616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0223400
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.9191.9514601
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9655467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30323.769130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10515519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6741523
X-RAY DIFFRACTIONr_chiral_restr0.3140.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212570
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.7881.52305
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.97723621
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.45531095
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.1534.5980
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.471→1.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 217 -
Rwork0.215 3986 -
obs--82.67 %

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