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- PDB-3mgj: Crystal structure of the Saccharop_dh_N domain of MJ1480 protein ... -

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Basic information

Entry
Database: PDB / ID: 3mgj
TitleCrystal structure of the Saccharop_dh_N domain of MJ1480 protein from Methanococcus jannaschii. Northeast Structural Genomics Consortium Target MjR83a.
ComponentsUncharacterized protein MJ1480
Keywordsstructural genomics / unknown function / Saccharop_dh_N domain / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyLOR/SDH bifunctional enzyme, conserved domain / Conserved hypothetical protein CHP00300 / LOR/SDH bifunctional enzyme, conserved domain / LOR/SDH bifunctional enzyme conserved region / DHS-like NAD/FAD-binding domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein MJ1480
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.703 Å
AuthorsVorobiev, S. / Neely, H. / Seetharaman, J. / Lee, D. / Patel, D. / Ciccosanti, C. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. ...Vorobiev, S. / Neely, H. / Seetharaman, J. / Lee, D. / Patel, D. / Ciccosanti, C. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the Saccharop_dh_N domain of MJ1480 protein from Methanococcus jannaschii.
Authors: Vorobiev, S. / Neely, H. / Seetharaman, J. / Lee, D. / Patel, D. / Xiao, R. / Ciccosanti, C. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionApr 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein MJ1480
B: Uncharacterized protein MJ1480


Theoretical massNumber of molelcules
Total (without water)28,1392
Polymers28,1392
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-9 kcal/mol
Surface area10440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.370, 65.395, 76.929
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsDimer according to aggregation screening

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Components

#1: Protein Uncharacterized protein MJ1480


Mass: 14069.513 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ1480 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +Magic / References: UniProt: Q58875
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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

Crystal growTemperature: 291 K / Method: microbatch under paraffin oil / pH: 4.2
Details: 2.21M lithium chloride, 0.1M sodium citrate, pH 4.2 , microbatch under paraffin oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 10525 / Num. obs: 10472 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 23.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1053 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXDEphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.703→33.155 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2549 480 4.6 %RANDOM
Rwork0.1992 ---
obs0.2018 10432 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.433 Å2 / ksol: 0.4 e/Å3
Refinement stepCycle: LAST / Resolution: 2.703→33.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1459 0 0 31 1490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011483
X-RAY DIFFRACTIONf_angle_d1.2611998
X-RAY DIFFRACTIONf_dihedral_angle_d20.069577
X-RAY DIFFRACTIONf_chiral_restr0.077226
X-RAY DIFFRACTIONf_plane_restr0.006263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7031-3.0940.32431730.24583312X-RAY DIFFRACTION100
3.094-3.89710.26451740.19183336X-RAY DIFFRACTION100
3.8971-33.1570.22251330.18933304X-RAY DIFFRACTION98
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.3804-0.3014-0.03020.68540.03351.56980.0848-0.02420.0287-0.1086-0.1360.1106-0.02940.14960.07020.23-0.00580.00570.23030.02240.2375-4.816861.341140.8279
21.61080.22221.49921.64890.75981.6110.05020.0371-0.0842-0.1405-0.08710.239-0.1126-0.21780.05110.18860.022-0.00280.2333-0.01190.2495
Refinement TLS groupSelection details: chain B

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