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- PDB-3un1: Crystal structure of an oxidoreductase from Sinorhizobium melilot... -

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Basic information

Entry
Database: PDB / ID: 3un1
TitleCrystal structure of an oxidoreductase from Sinorhizobium meliloti 1021
ComponentsProbable oxidoreductase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Function
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
PHOSPHATE ION / Probable oxidoreductase / Putative oxidoreductase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsAgarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Agarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of an oxidoreductase from Sinorhizobium meliloti 1021
Authors: Agarwal, R. / Almo, S.C. / Swaminathan, S.
History
DepositionNov 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable oxidoreductase
B: Probable oxidoreductase
C: Probable oxidoreductase
D: Probable oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5176
Polymers114,3274
Non-polymers1902
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14200 Å2
ΔGint-110 kcal/mol
Surface area31920 Å2
MethodPISA
2
A: Probable oxidoreductase
B: Probable oxidoreductase


Theoretical massNumber of molelcules
Total (without water)57,1642
Polymers57,1642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-38 kcal/mol
Surface area19990 Å2
MethodPISA
3
A: Probable oxidoreductase
D: Probable oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2593
Polymers57,1642
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-19 kcal/mol
Surface area20520 Å2
MethodPISA
4
B: Probable oxidoreductase
C: Probable oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2593
Polymers57,1642
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-20 kcal/mol
Surface area19960 Å2
MethodPISA
5
C: Probable oxidoreductase
D: Probable oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3544
Polymers57,1642
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-29 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.225, 84.225, 249.238
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Probable oxidoreductase / Putative oxidoreductase


Mass: 28581.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: y20210, RB0203, SM_b20210 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL
References: UniProt: Q9EXU6, UniProt: Q7ANT0*PLUS, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M MgCl2, 0.1M HEPES pH 7.5, 30% (v/v) PEG550MME, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2011 / Details: mirrors
RadiationMonochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 38775 / Num. obs: 38775 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 21.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 21.2 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 4 / Num. unique all: 3804 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D3W

3d3w


Resolution: 2.45→47.38 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.596 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.442 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24062 1939 5 %RANDOM
Rwork0.18486 ---
obs0.18764 36644 99.69 %-
all-38775 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.217 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.45→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7034 0 10 158 7202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0217167
X-RAY DIFFRACTIONr_angle_refined_deg1.8811.9469723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7925942
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44223.01299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.378151141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4351562
X-RAY DIFFRACTIONr_chiral_restr0.1280.21122
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215433
X-RAY DIFFRACTIONr_mcbond_it0.9971.54662
X-RAY DIFFRACTIONr_mcangle_it1.92327478
X-RAY DIFFRACTIONr_scbond_it3.33832505
X-RAY DIFFRACTIONr_scangle_it5.5224.52245
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 139 -
Rwork0.22 2652 -
obs--99.61 %

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