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- PDB-3vc7: Crystal Structure of a putative oxidoreductase from Sinorhizobium... -

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Basic information

Entry
Database: PDB / ID: 3vc7
TitleCrystal Structure of a putative oxidoreductase from Sinorhizobium meliloti 1021
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity / nucleotide binding
Similarity search - Function
PKS_KR / 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
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.231 Å
AuthorsGhosh, A. / Bhoshle, R. / Toro, R. / Gizzi, A. / Hillerich, B. / Seidel, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal Structure of a putative oxidoreductase protein from Sinorhizobium meliloti 1021
Authors: Ghosh, A. / Bhoshle, R. / Toro, R. / Gizzi, A. / Hillerich, B. / Almo, S.C.
History
DepositionJan 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Other
Revision 1.2Sep 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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative oxidoreductase
B: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5574
Polymers53,3732
Non-polymers1842
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-28 kcal/mol
Surface area20240 Å2
MethodPISA
2
A: Putative oxidoreductase
hetero molecules

A: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5574
Polymers53,3732
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3210 Å2
ΔGint-24 kcal/mol
Surface area20210 Å2
MethodPISA
3
B: Putative oxidoreductase
hetero molecules

B: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5574
Polymers53,3732
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2910 Å2
ΔGint-26 kcal/mol
Surface area20850 Å2
MethodPISA
4
A: Putative oxidoreductase
B: Putative oxidoreductase
hetero molecules

A: Putative oxidoreductase
B: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,1158
Polymers106,7464
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13520 Å2
ΔGint-101 kcal/mol
Surface area33660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.074, 119.301, 64.128
Angle α, β, γ (deg.)90.00, 110.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative oxidoreductase


Mass: 26686.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: GI: 15966075, R02322, SMc01571 / Plasmid: CHS30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pRIL / References: UniProt: Q92N93, Oxidoreductases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 1.99 Å3/Da / Density % sol: 38.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 200 mM MgCl2, 100 mM Tris, and 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2011
RadiationMonochromator: Rosenbaum-Rock double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 39837 / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 32.3 Å2
Reflection shellResolution: 2.25→2.29 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EMK

3emk


Resolution: 2.231→32.322 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / σ(I): -1 / Phase error: 24.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1035 5.13 %RANDOM
Rwork0.1796 ---
obs0.1821 20178 99.34 %-
all-20316 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.838 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.199 Å20 Å2-4.8613 Å2
2--3.9955 Å20 Å2
3----6.1946 Å2
Refinement stepCycle: LAST / Resolution: 2.231→32.322 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 0 12 109 3631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043568
X-RAY DIFFRACTIONf_angle_d0.8334819
X-RAY DIFFRACTIONf_dihedral_angle_d14.1581281
X-RAY DIFFRACTIONf_chiral_restr0.058564
X-RAY DIFFRACTIONf_plane_restr0.003633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.231-2.34850.2921440.24872635X-RAY DIFFRACTION96
2.3485-2.49560.28611590.22812726X-RAY DIFFRACTION100
2.4956-2.68820.30841460.21222750X-RAY DIFFRACTION100
2.6882-2.95860.24981290.19772753X-RAY DIFFRACTION100
2.9586-3.38630.23471590.16712746X-RAY DIFFRACTION100
3.3863-4.26490.1831330.15032768X-RAY DIFFRACTION100
4.2649-32.32510.20081650.16562765X-RAY DIFFRACTION100
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)
14.1285-1.37540.58672.2628-1.34475.5642-0.09180.16810.3609-0.20670.03760.3568-0.6608-0.2765-0.00760.48950.0325-0.12270.22220.06640.294-9.108810.5222-17.4101
21.25340.12960.25052.01570.00721.4952-0.09150.24480.1045-0.44560.09350.1659-0.11860.0339-0.02790.2571-0.0095-0.04520.20460.02780.1505-4.7682-6.7312-18.0735
31.6002-0.96431.02671.85160.24742.9649-0.0142-0.00250.16190.01250.06890.4592-0.2637-0.444-0.01040.18780.0308-0.00990.17050.00830.2106-10.8555-2.884-1.2441
42.8669-0.50540.01674.85490.03055.82790.09190.1619-0.2660.15170.067-0.32920.04790.3927-0.06040.3787-0.0377-0.0890.1381-0.02840.1648-3.6067-43.5697-15.5884
55.215-0.98271.3223.7419-0.44043.1670.0460.5982-0.4394-0.73430.0274-0.21120.4170.2117-0.090.4884-0.0115-0.0650.267-0.08220.2638-7.1615-41.7325-26.3615
60.61390.1010.50432.0003-0.03451.8627-0.0230.130.0396-0.37310.0566-0.04740.01690.1631-0.02830.2398-0.0027-0.00750.1791-0.0230.113-1.3316-26.7342-15.1592
74.3835-0.1362-1.43972.9187-0.56683.2456-0.01130.1228-0.2582-0.2374-0.0039-0.06260.32360.1258-0.00630.1450.0121-0.06470.09530.00560.08511.7568-32.3303-3.3831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 4:59)
2X-RAY DIFFRACTION2chain 'A' and (resseq 60:180)
3X-RAY DIFFRACTION3chain 'A' and (resseq 181:251)
4X-RAY DIFFRACTION4chain 'B' and (resseq 2:39)
5X-RAY DIFFRACTION5chain 'B' and (resseq 40:77)
6X-RAY DIFFRACTION6chain 'B' and (resseq 78:216)
7X-RAY DIFFRACTION7chain 'B' and (resseq 217:251)

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