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- PDB-1jeo: Crystal Structure of the Hypothetical Protein MJ1247 from Methano... -

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Basic information

Entry
Database: PDB / ID: 1jeo
TitleCrystal Structure of the Hypothetical Protein MJ1247 from Methanococcus jannaschii at 2.0 A Resolution Infers a Molecular Function of 3-Hexulose-6-Phosphate isomerase.
ComponentsHYPOTHETICAL PROTEIN MJ1247
KeywordsISOMERASE / RuMP pathway / phosphosugar / 3-hexulose-6-phosphate isomerase / PHI / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


6-phospho-3-hexuloisomerase / 6-phospho-3-hexuloisomerase activity / carbohydrate derivative metabolic process / carbohydrate derivative binding
Similarity search - Function
3-hexulose-6-phosphate isomerase / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / 3-hexulose-6-phosphate isomerase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMartinez-Cruz, L.A. / Dreyer, M.K. / Boisvert, D.C. / Yokota, H. / Martinez-Chantar, M.L. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Structure / Year: 2002
Title: Crystal structure of MJ1247 protein from M. jannaschii at 2.0 A resolution infers a molecular function of 3-hexulose-6-phosphate isomerase.
Authors: Martinez-Cruz, L.A. / Dreyer, M.K. / Boisvert, D.C. / Yokota, H. / Martinez-Chantar, M.L. / Kim, R. / Kim, S.H.
History
DepositionJun 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 3, 2024Group: 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 1.4Nov 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: HYPOTHETICAL PROTEIN MJ1247
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8912
Polymers20,6981
Non-polymers1921
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: HYPOTHETICAL PROTEIN MJ1247
hetero molecules

A: HYPOTHETICAL PROTEIN MJ1247
hetero molecules

A: HYPOTHETICAL PROTEIN MJ1247
hetero molecules

A: HYPOTHETICAL PROTEIN MJ1247
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5628
Polymers82,7944
Non-polymers7684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_657-x+1,y,-z+21
crystal symmetry operation4_577x,-y+2,-z+21
Buried area16660 Å2
ΔGint-118 kcal/mol
Surface area24680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)67.921, 68.155, 83.336
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations -X,-Y, Z X,-Y,-Z -X, Y,-Z

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Components

#1: Protein HYPOTHETICAL PROTEIN MJ1247 / MJ1247


Mass: 20698.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: mj1247 / Plasmid: SJS1244 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q58644
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 40% PEG 400, 0.1 M Tris/HCl, 0.2 M Sodium citrate, 10 mM betamercaptoethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
140 %PEG4001reservoir
20.1 MTris-HCl1reservoirpH8.5
30.2 Msodium citrate1reservoir
410 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 37198 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.44 % / Biso Wilson estimate: 19.03 Å2 / Rsym value: 0.08 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.63 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.98 / Num. unique all: 982 / Rsym value: 0.32 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 12655 / % possible obs: 94 % / Num. measured all: 37198 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 75.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
EPMRphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MJ1247 model obtained from MAD data (selenomethionine-derivatized crystals)

Resolution: 2→30 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: RESIDUES 1-3 ARE DISORDERED. HENCE, THE COORDINATES OF ITS SIDE CHAIN ARE NOT INCLUDED IN THE PDB FILE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 650 5.4 %RANDOM
Rwork0.1891 ---
all0.1903 ---
obs0.1903 11995 89.5 %-
Displacement parametersBiso mean: 18.4695 Å2
Baniso -1Baniso -2Baniso -3
1--3.117 Å20 Å20 Å2
2--0.986 Å20 Å2
3---2.131 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1423 0 13 72 1508
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2-2.050.3816380.2876X-RAY DIFFRACTION738
2.05-2.110.2789560.2571X-RAY DIFFRACTION854
2.11-2.180.2717390.2436X-RAY DIFFRACTION904
2.18-2.260.3216380.225X-RAY DIFFRACTION930
2.26-2.350.2511430.2178X-RAY DIFFRACTION944
2.35-2.460.2873540.2197X-RAY DIFFRACTION916
2.46-2.590.1911590.1981X-RAY DIFFRACTION921
2.75-2.960.2438430.1932X-RAY DIFFRACTION946
3.26-3.730.201490.158X-RAY DIFFRACTION967
3.73-4.70.192540.1572X-RAY DIFFRACTION966
4.7-300.1822570.1658X-RAY DIFFRACTION1007
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.1891
Solvent computation
*PLUS
Displacement parameters
*PLUS

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