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- PDB-3sxw: Crystal Structure of Engineered Protein. Northeast Structural Gen... -

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Basic information

Entry
Database: PDB / ID: 3sxw
TitleCrystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR69.
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / Engineered protein / Structural Genomics / PSI-biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / gluconeogenesis / glycolytic process / iron ion binding / cytoplasm
Similarity search - Function
Glucose-6-phosphate isomerase, prokaryote / Glucose-6-phosphate isomerase, archaea/bacteria / Glucose-6-phosphate isomerase (GPI) / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsVorobiev, S. / Su, M. / Nivon, L. / Seetharaman, J. / Patel, P. / Xiao, R. / Maglaqui, M. / Ciccosanti, C. / Baker, D. / Everett, J.K. ...Vorobiev, S. / Su, M. / Nivon, L. / Seetharaman, J. / Patel, P. / Xiao, R. / Maglaqui, M. / Ciccosanti, C. / Baker, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR69.
Authors: Vorobiev, S. / Su, M. / Nivon, L. / Seetharaman, J. / Patel, P. / Xiao, R. / Maglaqui, M. / Ciccosanti, C. / Baker, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. ...Authors: Vorobiev, S. / Su, M. / Nivon, L. / Seetharaman, J. / Patel, P. / Xiao, R. / Maglaqui, M. / Ciccosanti, C. / Baker, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJul 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucose-6-phosphate isomerase


Theoretical massNumber of molelcules
Total (without water)22,7721
Polymers22,7721
Non-polymers00
Water2,954164
1
A: Glucose-6-phosphate isomerase

A: Glucose-6-phosphate isomerase


Theoretical massNumber of molelcules
Total (without water)45,5442
Polymers45,5442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3680 Å2
ΔGint-31 kcal/mol
Surface area16310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.131, 59.131, 137.630
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Detailsdimer,50.85 kD,94.4%|tetramer,102.5 kD,2.3%

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Components

#1: Protein Glucose-6-phosphate isomerase / / GPI / Phosphoglucose isomerase / PGI / Phosphohexose isomerase / PHI


Mass: 22771.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: pgiA, PF0196 / References: UniProt: P83194, glucose-6-phosphate isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3.05 Å3/Da / Density % sol: 59.67 %
Crystal growTemperature: 291 K / Method: microbatch crystallization under oil / pH: 5
Details: 18-22% PEG 8000, 0.1 M Manganese sulfate, 0.1 M Sodium acetate, pH 5.0 , Microbatch crystallization under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97915 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 8, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 99736 / Num. obs: 99636 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 29.73 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 26.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 1.56 / Num. unique all: 9946 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1x82

1x82


Resolution: 1.801→34.17 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.883 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.16 / Phase error: 18.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2512 5.05 %RANDOM
Rwork0.176 ---
obs0.178 49787 99.91 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.687 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 91.52 Å2 / Biso mean: 36.386 Å2 / Biso min: 19.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.748 Å2-0 Å2-0 Å2
2--1.748 Å2-0 Å2
3----3.497 Å2
Refinement stepCycle: LAST / Resolution: 1.801→34.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1482 0 0 164 1646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081522
X-RAY DIFFRACTIONf_angle_d1.1012061
X-RAY DIFFRACTIONf_chiral_restr0.08214
X-RAY DIFFRACTIONf_plane_restr0.004268
X-RAY DIFFRACTIONf_dihedral_angle_d15.262553
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.801-1.8350.2541240.2826132737100
1.835-1.8730.3691530.2926432796100
1.873-1.9130.2881420.23926342776100
1.913-1.9580.2711230.20626092732100
1.958-2.0070.2211360.18426452781100
2.007-2.0610.1971490.18225982747100
2.061-2.1220.2291470.17926502797100
2.122-2.190.2081350.17226512786100
2.19-2.2690.1991460.17426392785100
2.269-2.3590.2181370.18126132750100
2.359-2.4670.2051580.1826142772100
2.467-2.5970.2661350.18626132748100
2.597-2.7590.2431880.18925632751100
2.759-2.9720.2161380.18926552793100
2.972-3.2710.2111360.17126262762100
3.271-3.7440.1831170.15926552772100
3.744-4.7150.1751240.14126312755100
4.715-34.1760.2311240.1842623274799

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