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- PDB-4luk: The crystal structure of the P132A, Y133G mutant of Pyrococcus fu... -

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Basic information

Entry
Database: PDB / ID: 4luk
TitleThe crystal structure of the P132A, Y133G mutant of Pyrococcus furiosus phosphoglucose isomerase in complex with manganese and 5-phospho-D-arabinonate.
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / Cupin Fold / Glucose 6-phsphate and Fructose 6-phosphate binding protein
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glycolytic process / gluconeogenesis / 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
: / 5-PHOSPHOARABINONIC ACID / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsBaker, P.J. / Almourfi, F.M.
CitationJournal: To be Published
Title: Correlated mutation analysis as a tool for smart library design to improve protein performance.
Authors: Baker, P.J. / Almourfi, F.M. / Raedts, J. / Joosten, H.-J. / Hendriks, S. / Kengen, S.W.M. / Hage, W.R. / Schaap, P.J. / Sedelnikova, S.E. / Van der Oost, J.
History
DepositionJul 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / 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_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.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_atom_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.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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9237
Polymers21,3731
Non-polymers5496
Water3,513195
1
A: Glucose-6-phosphate isomerase
hetero molecules

A: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,84514
Polymers42,7472
Non-polymers1,09912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6110 Å2
ΔGint-34 kcal/mol
Surface area17260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.850, 43.280, 58.450
Angle α, β, γ (deg.)90.00, 122.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-495-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: -X, Y, -Z

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Components

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


Mass: 21373.275 Da / Num. of mol.: 1 / Mutation: P132A, Y133G
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 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P83194, glucose-6-phosphate isomerase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Sugar ChemComp-PA5 / 5-PHOSPHOARABINONIC ACID


Type: saccharide / Mass: 246.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O9P
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.18 Å3/Da / Density % sol: 43.64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.35 M MgCl2, 0.1 M sodium acetate PH 5.5 and 19% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2011 / Details: Diamond IO3
RadiationMonochromator: Diamond IO3 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.41→28.92 Å / Num. all: 32797 / Num. obs: 32797 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 13
Reflection shellResolution: 1.41→1.44 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1460 / % possible all: 55.4

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.5.0109refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X7N

1x7n


Resolution: 1.41→28.92 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.172 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21388 1663 5.1 %RANDOM
Rwork0.15009 ---
obs0.15336 31134 100 %-
all-32797 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.299 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å2-1.83 Å2
2--2.35 Å20 Å2
3----2.56 Å2
Refinement stepCycle: LAST / Resolution: 1.41→28.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 32 195 1737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221576
X-RAY DIFFRACTIONr_bond_other_d0.0010.021096
X-RAY DIFFRACTIONr_angle_refined_deg1.0641.9672122
X-RAY DIFFRACTIONr_angle_other_deg0.72632666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.06824.52173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.58715266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.722156
X-RAY DIFFRACTIONr_chiral_restr0.0630.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211728
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02322
X-RAY DIFFRACTIONr_mcbond_it37.2211.5934
X-RAY DIFFRACTIONr_mcbond_other21.171.5387
X-RAY DIFFRACTIONr_mcangle_it35.50421503
X-RAY DIFFRACTIONr_scbond_it86.293642
X-RAY DIFFRACTIONr_scangle_it78.1634.5619
X-RAY DIFFRACTIONr_rigid_bond_restr52.30232672
LS refinement shellResolution: 1.406→1.443 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 72 -
Rwork0.326 1386 -
obs--100 %

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