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- PDB-2b0a: Crystal structure of protein MJ0783 from Methanococcus jannaschii -

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Basic information

Entry
Database: PDB / ID: 2b0a
TitleCrystal structure of protein MJ0783 from Methanococcus jannaschii
ComponentsHypothetical protein MJ0783
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / HYPOTHETICAL PROTEIN / PSI / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


arylformamidase activity / L-tryptophan catabolic process to kynurenine
Similarity search - Function
Putative cyclase / Kynurenine formamidase/cyclase-like / Kynurenine formamidase superfamily / Putative cyclase / Glucose Oxidase; domain 1 / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein MJ0783
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsPatskovsky, Y. / Ramagopal, U. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Hypothetical Protein Mj0783 from Methanococcus Jannaschii
Authors: Patskovsky, Y. / Ramagopal, U. / Almo, S.C.
History
DepositionSep 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / pdbx_struct_special_symmetry / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein MJ0783


Theoretical massNumber of molelcules
Total (without water)21,1231
Polymers21,1231
Non-polymers00
Water2,270126
1
A: Hypothetical protein MJ0783

A: Hypothetical protein MJ0783


Theoretical massNumber of molelcules
Total (without water)42,2452
Polymers42,2452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4190 Å2
ΔGint-28 kcal/mol
Surface area16210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)67.942, 73.156, 46.570
Angle α, β, γ (deg.)90.00, 122.87, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-249-

HOH

21A-281-

HOH

31A-286-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: -x+1, y, -z+1

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Components

#1: Protein Hypothetical protein MJ0783


Mass: 21122.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0783 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q58193
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.46 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 550, 100 mM Tris-HCl, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 87 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.29 / Wavelength: 0.989 Å
DetectorType: ADSC QUANTAM Q315 / Detector: CCD / Date: Sep 2, 2005 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.291
20.9891
ReflectionResolution: 1.45→50 Å / Num. all: 34059 / Num. obs: 34059 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Rsym value: 0.063 / Net I/σ(I): 16.1
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.35 / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SHELXmodel building
REFMAC5.2.0005refinement
HKL-2000data reduction
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.45→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.359 / SU ML: 0.053 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21823 1052 3.2 %RANDOM
Rwork0.18505 ---
obs0.18608 32334 98.12 %-
all-32334 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.091 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å2-1.74 Å2
2--0.13 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 0 126 1613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221558
X-RAY DIFFRACTIONr_bond_other_d0.0010.021468
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9952113
X-RAY DIFFRACTIONr_angle_other_deg0.64933439
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6515195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.94524.49369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93115291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.381158
X-RAY DIFFRACTIONr_chiral_restr0.080.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021707
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02304
X-RAY DIFFRACTIONr_nbd_refined0.2190.3294
X-RAY DIFFRACTIONr_nbd_other0.1930.31471
X-RAY DIFFRACTIONr_nbtor_refined0.1840.5772
X-RAY DIFFRACTIONr_nbtor_other0.0870.5970
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.5176
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2330.357
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.516
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.79121253
X-RAY DIFFRACTIONr_mcbond_other1.0952384
X-RAY DIFFRACTIONr_mcangle_it5.13131545
X-RAY DIFFRACTIONr_scbond_it5.1722713
X-RAY DIFFRACTIONr_scangle_it6.7843564
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.448→1.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 77 -
Rwork0.252 2335 -
obs--95.87 %

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