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- PDB-4lum: The crystal structure of the P132V mutant of Pyrococcus furiosus ... -

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Basic information

Entry
Database: PDB / ID: 4lum
TitleThe crystal structure of the P132V mutant of Pyrococcus furiosus phosphoglucose isomerase in complex with manganese and fructose-6- phosphate.
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / Cupin Fold / Glucose 6-phosphate and Fructose 6-phosphate binding protein
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
FRUCTOSE -6-PHOSPHATE / : / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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)43,9076
Polymers43,2772
Non-polymers6304
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-50 kcal/mol
Surface area16950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.940, 45.010, 48.690
Angle α, β, γ (deg.)87.81, 89.86, 75.47
Int Tables number1
Space group name H-MP1
DetailsThe asymmetric unit contains the biological dimer.

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Components

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


Mass: 21638.648 Da / Num. of mol.: 2 / Mutation: P132V
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.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-F6R / FRUCTOSE -6-PHOSPHATE / Fructose 6-phosphate


Mass: 260.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13O9P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium nitrate, 0.1 M Bis Tris Propane PH6.5, 20% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2011 / Details: Diamond I03
RadiationMonochromator: Diamond I03 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.79→18.49 Å / Num. all: 33074 / Num. obs: 33074 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 4.3
Reflection shellResolution: 1.79→1.84 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2386 / % possible all: 94

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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: 1.79→18.49 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.138 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.451 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22008 1675 5.1 %RANDOM
Rwork0.17325 ---
obs0.17577 31398 100 %-
all-33074 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.347 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å21.08 Å20.42 Å2
2---0.37 Å2-0.37 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.79→18.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3056 0 34 218 3308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223168
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9644282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4215378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88124.459148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21415542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5491512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212406
X-RAY DIFFRACTIONr_mcbond_it0.9971.51880
X-RAY DIFFRACTIONr_mcangle_it1.85123032
X-RAY DIFFRACTIONr_scbond_it2.62131288
X-RAY DIFFRACTIONr_scangle_it4.3524.51250
X-RAY DIFFRACTIONr_rigid_bond_restr1.24233168
LS refinement shellResolution: 1.794→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 119 -
Rwork0.211 2240 -
obs--100 %

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