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- PDB-6oz7: Putative oxidoreductase from Escherichia coli str. K-12 -

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Basic information

Entry
Database: PDB / ID: 6oz7
TitlePutative oxidoreductase from Escherichia coli str. K-12
ComponentsUncharacterized oxidoreductase YohF
KeywordsOXIDOREDUCTASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity
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
TRIETHYLENE GLYCOL / Uncharacterized oxidoreductase YohF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsOsipiuk, J. / Skarina, T. / Mesa, N. / Endres, M. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: to be published
Title: Putative oxidoreductase from Escherichia coli str. K-12
Authors: Osipiuk, J. / Skarina, T. / Mesa, N. / Endres, M. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized oxidoreductase YohF
B: Uncharacterized oxidoreductase YohF
C: Uncharacterized oxidoreductase YohF
D: Uncharacterized oxidoreductase YohF
E: Uncharacterized oxidoreductase YohF
F: Uncharacterized oxidoreductase YohF
G: Uncharacterized oxidoreductase YohF
H: Uncharacterized oxidoreductase YohF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,19021
Polymers216,3828
Non-polymers80713
Water32,4271800
1
C: Uncharacterized oxidoreductase YohF
D: Uncharacterized oxidoreductase YohF
hetero molecules

A: Uncharacterized oxidoreductase YohF
B: Uncharacterized oxidoreductase YohF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,65210
Polymers108,1914
Non-polymers4616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area16280 Å2
ΔGint-142 kcal/mol
Surface area31150 Å2
MethodPISA
2
E: Uncharacterized oxidoreductase YohF
F: Uncharacterized oxidoreductase YohF
G: Uncharacterized oxidoreductase YohF
H: Uncharacterized oxidoreductase YohF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,53811
Polymers108,1914
Non-polymers3477
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16910 Å2
ΔGint-131 kcal/mol
Surface area31060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.819, 72.210, 119.945
Angle α, β, γ (deg.)82.590, 87.030, 67.820
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Uncharacterized oxidoreductase YohF


Mass: 27047.791 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: yohF, yohE, b2137, JW2125 / Variant: K-12 substr. MG1655 / Plasmid: pMCSG53
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P33368, Oxidoreductases
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 1800 / 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: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 28% PEG 400, 0.2M CaCl2, 0.1M Hepes buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.36→48.14 Å / Num. obs: 320625 / % possible obs: 88.3 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.031 / Rrim(I) all: 0.052 / Χ2: 1.236 / Net I/av σ(I): 22.4 / Net I/σ(I): 16.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.36-1.382.10.5161.4478020.5910.4210.6690.8743.2
1.38-1.412.20.40793550.7410.330.5260.70951.3
1.41-1.442.20.343110360.7970.2790.4440.71860.8
1.44-1.472.10.305138390.820.250.3960.83276.3
1.47-1.52.10.254168240.8610.2070.3290.8792.8
1.5-1.532.30.232170490.9390.1880.2991.10293.7
1.53-1.572.50.18173100.9360.1420.230.90194.7
1.57-1.612.60.144172430.9580.1130.1840.93695
1.61-1.662.60.124172620.9660.0980.1591.01495.3
1.66-1.712.60.11174170.9750.0860.141.07895.6
1.71-1.772.60.09173470.9820.0710.1151.19695.7
1.77-1.852.60.075174250.9880.0580.0951.27596.1
1.85-1.932.60.072173130.9840.0570.0931.72495.3
1.93-2.032.60.054175070.9930.0420.0691.57296.3
2.03-2.162.60.047174250.9940.0360.061.68496.1
2.16-2.332.60.042174360.9940.0330.0541.70495.9
2.33-2.562.60.034177400.9970.0260.0431.35197.7
2.56-2.932.60.032178470.9970.0240.041.28698.1
2.93-3.692.60.029178430.9970.0220.0371.26398.2
3.69-48.142.60.032176050.9970.0240.041.42796.9

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DML

4dml


Resolution: 1.36→48.14 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.206 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.057
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1692 15748 4.9 %RANDOM
Rwork0.1232 ---
obs0.1255 304841 88.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 91.25 Å2 / Biso mean: 19.197 Å2 / Biso min: 8.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å2-0.37 Å20.36 Å2
2---0.61 Å2-0.36 Å2
3---0.12 Å2
Refinement stepCycle: final / Resolution: 1.36→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14289 0 40 1801 16130
Biso mean--35.9 32.92 -
Num. residues----1912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01315407
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714793
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.62821071
X-RAY DIFFRACTIONr_angle_other_deg1.5041.57134376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99552124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.34122.802753
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.703152624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9991594
X-RAY DIFFRACTIONr_chiral_restr0.0880.22121
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217614
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023068
X-RAY DIFFRACTIONr_rigid_bond_restr2.046330200
LS refinement shellResolution: 1.359→1.394 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 607 -
Rwork0.251 11267 -
all-11874 -
obs--44.14 %

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