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- PDB-3nbu: Crystal structure of pGI glucosephosphate isomerase -

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Basic information

Entry
Database: PDB / ID: 3nbu
TitleCrystal structure of pGI glucosephosphate isomerase
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / monosaccharide binding / gluconeogenesis / glycolytic process / cellular response to oxidative stress / identical protein binding / cytosol
Similarity search - Function
Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. ...Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsAlber, T. / Zubieta, C. / Totir, M. / May, A. / Echols, N.
CitationJournal: Plos One / Year: 2012
Title: Macro-to-Micro Structural Proteomics: Native Source Proteins for High-Throughput Crystallization.
Authors: Totir, M. / Echols, N. / Nanao, M. / Gee, C.L. / Moskaleva, A. / Gradia, S. / Iavarone, A.T. / Berger, J.M. / May, A.P. / Zubieta, C. / Alber, T.
History
DepositionJun 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Sep 6, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase
C: Glucose-6-phosphate isomerase
D: Glucose-6-phosphate isomerase
E: Glucose-6-phosphate isomerase
F: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)369,8257
Polymers369,7896
Non-polymers351
Water58,7653262
1
A: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase


Theoretical massNumber of molelcules
Total (without water)123,2632
Polymers123,2632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12550 Å2
ΔGint-69 kcal/mol
Surface area35300 Å2
MethodPISA
2
C: Glucose-6-phosphate isomerase
D: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,2983
Polymers123,2632
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12710 Å2
ΔGint-80 kcal/mol
Surface area34880 Å2
MethodPISA
3
E: Glucose-6-phosphate isomerase
F: Glucose-6-phosphate isomerase


Theoretical massNumber of molelcules
Total (without water)123,2632
Polymers123,2632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12520 Å2
ΔGint-69 kcal/mol
Surface area35130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.806, 72.874, 181.851
Angle α, β, γ (deg.)92.47, 97.82, 114.57
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 61631.516 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: DH5a / References: UniProt: P0A6T1, glucose-6-phosphate isomerase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3262 / 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: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.2M ammonium acetate, 0.1M Bis-Tris 5.5, 10 mM betaine HCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2007 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.99→89 Å / Num. all: 208294 / Num. obs: 208294 / % possible obs: 94.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 9.7
Reflection shellResolution: 1.99→2.1 Å / Redundancy: 2 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 1.7 / Num. unique all: 29607 / Rsym value: 0.423 / % possible all: 94.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dqr

1dqr


Resolution: 2.05→89 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.651 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22952 9609 5 %RANDOM
Rwork0.16923 ---
obs0.17227 181581 94.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.059 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å2-1.16 Å2-0.82 Å2
2---1.03 Å2-1.09 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 2.05→89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25984 0 1 3262 29247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02226613
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.93336077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79753283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21924.6911277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.144154435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9415108
X-RAY DIFFRACTIONr_chiral_restr0.0950.23945
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02120358
X-RAY DIFFRACTIONr_mcbond_it0.9851.516323
X-RAY DIFFRACTIONr_mcangle_it1.689226252
X-RAY DIFFRACTIONr_scbond_it3.045310290
X-RAY DIFFRACTIONr_scangle_it4.5774.59825
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 692 -
Rwork0.273 13225 -
obs--93.57 %

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