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- PDB-3ff1: Structure of Glucose 6-phosphate Isomerase from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 3ff1
TitleStructure of Glucose 6-phosphate Isomerase from Staphylococcus aureus
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / Alpha Beta / Rossmann fold / Glucose-6-phosphate isomerase like protein / Gluconeogenesis / Glycolysis / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm
Similarity search - Function
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 ...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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUCOSE-6-PHOSPHATE / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsAnderson, S.M. / Brunzelle, J.S. / Onopriyenko, O. / Peterson, S. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Structure of Glucose 6-phosphate Isomerase from Staphylococcus aureus
Authors: Anderson, S.M. / Brunzelle, J.S. / Onopriyenko, O. / Peterson, S. / Anderson, W.F. / Savchenko, A.
History
DepositionDec 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4607
Polymers101,1082
Non-polymers3525
Water25,3111405
1
A: Glucose-6-phosphate isomerase
hetero molecules

A: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1544
Polymers101,1082
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11190 Å2
ΔGint-76 kcal/mol
Surface area31120 Å2
MethodPISA
2
A: Glucose-6-phosphate isomerase
hetero molecules

A: Glucose-6-phosphate isomerase
hetero molecules

B: Glucose-6-phosphate isomerase
hetero molecules

B: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,92114
Polymers202,2174
Non-polymers70410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation3_555-y+1/2,x+1/2,z+1/41
crystal symmetry operation6_554x+1/2,-y+1/2,-z-1/41
Buried area25670 Å2
ΔGint-154 kcal/mol
Surface area58100 Å2
MethodPISA
3
B: Glucose-6-phosphate isomerase
hetero molecules

B: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,76710
Polymers101,1082
Non-polymers6588
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area10970 Å2
ΔGint-75 kcal/mol
Surface area30500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.267, 163.267, 103.732
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1384-

HOH

21A-1387-

HOH

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Components

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


Mass: 50554.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: COL / Gene: pgi, SACOL0966 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HHC2, glucose-6-phosphate isomerase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-G6Q / GLUCOSE-6-PHOSPHATE / Glucose 6-phosphate


Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1405 / 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: 3.44 Å3/Da / Density % sol: 64.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 1.4M Sodium Citrate, 0.1M Hepes pH 7.5, 10mM Glucose-6-Phosphate, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97931 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 27, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionRedundancy: 12.3 % / Av σ(I) over netI: 16.71 / Number: 2196924 / Rmerge(I) obs: 0.096 / Χ2: 1.46 / D res high: 2 Å / D res low: 50 Å / Num. obs: 178453 / % possible obs: 98.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.315099.910.0512.113.1
3.424.3110010.0622.22413.1
2.993.4210010.0781.75213.1
2.712.9910010.1091.61713.1
2.522.7110010.131.25113.1
2.372.5210010.1621.13813
2.252.3710010.2021.08612.9
2.152.2510010.2331.05612.7
2.072.1598.610.2781.03410.6
22.0790.210.3290.9698.1
ReflectionResolution: 1.65→50 Å / Num. all: 1674949 / Num. obs: 164480 / % possible obs: 98.2 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 3.3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.108 / Χ2: 1.002 / Net I/σ(I): 16.711
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.715.10.401141891.005185.9
1.71-1.786.40.363160150.997196.6
1.78-1.867.60.3165561.029199.9
1.86-1.968.10.223166161.0051100
1.96-2.088.30.168166391.0061100
2.08-2.248.30.135166371.0091100
2.24-2.468.40.119167020.9891100
2.46-2.828.30.099167761.0181100
2.82-3.558.30.09169091.0011100
3.55-5080.083174410.965199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0044refinement
PDB_EXTRACT3.006data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→46.22 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.181 / WRfactor Rwork: 0.153 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.905 / SU R Cruickshank DPI: 0.066 / SU Rfree: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17 8278 5 %RANDOM
Rwork0.146 156098 --
obs0.148 164376 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 78.12 Å2 / Biso mean: 19.399 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→46.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7042 0 20 1405 8467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227375
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.96310003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6435928
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88625.41366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.239151300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6741526
X-RAY DIFFRACTIONr_chiral_restr0.1270.21090
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215662
X-RAY DIFFRACTIONr_mcbond_it1.34824485
X-RAY DIFFRACTIONr_mcangle_it2.23737246
X-RAY DIFFRACTIONr_scbond_it2.40322890
X-RAY DIFFRACTIONr_scangle_it3.54432743
LS refinement shellResolution: 1.649→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 531 -
Rwork0.243 9647 -
all0.244 10178 -
obs--83.47 %

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