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- PDB-5yga: Crystal structure of ribose-1,5-bisphosphate isomerase mutant D20... -

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Basic information

Entry
Database: PDB / ID: 5yga
TitleCrystal structure of ribose-1,5-bisphosphate isomerase mutant D204N from Pyrococcus horikoshii OT3 in complex with ribose-1,5-bisphosphate, AMP and GMP
ComponentsRibose 1,5-bisphosphate isomerase
KeywordsISOMERASE / NMP degradation pathway / Ribose-1 / 5-bisphosphate / Rossmann-like fold
Function / homology
Function and homology information


ribose-1,5-bisphosphate isomerase / ribose 1,5-bisphosphate isomerase activity / S-methyl-5-thioribose-1-phosphate isomerase activity / pentose catabolic process / L-methionine salvage from methylthioadenosine
Similarity search - Function
Ribose-1,5-bisphosphate isomerase, e2b2 family / Initiation factor 2B alpha/beta/delta / translation initiation factor eif-2b, domain 1 / Methylthioribose-1-phosphate isomerase, N-terminal / Translation initiation factor eif-2b; domain 2 / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / NagB/RpiA transferase-like / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Ribose-1,5-bisphosphate isomerase, e2b2 family / Initiation factor 2B alpha/beta/delta / translation initiation factor eif-2b, domain 1 / Methylthioribose-1-phosphate isomerase, N-terminal / Translation initiation factor eif-2b; domain 2 / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / NagB/RpiA transferase-like / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / ADENOSINE MONOPHOSPHATE / : / 1,5-di-O-phosphono-alpha-D-ribofuranose / Ribose 1,5-bisphosphate isomerase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsGogoi, P. / Kanaujia, S.P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT)BT/302/NE/TBP/2012 dated 07.01.2013 India
CitationJournal: Sci Rep / Year: 2018
Title: A presumed homologue of the regulatory subunits of eIF2B functions as ribose-1,5-bisphosphate isomerase in Pyrococcus horikoshii OT3.
Authors: Gogoi, P. / Kanaujia, S.P.
History
DepositionSep 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0May 29, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / software
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribose 1,5-bisphosphate isomerase
B: Ribose 1,5-bisphosphate isomerase
C: Ribose 1,5-bisphosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,30015
Polymers109,3663
Non-polymers2,93412
Water5,423301
1
A: Ribose 1,5-bisphosphate isomerase
B: Ribose 1,5-bisphosphate isomerase
C: Ribose 1,5-bisphosphate isomerase
hetero molecules

A: Ribose 1,5-bisphosphate isomerase
B: Ribose 1,5-bisphosphate isomerase
C: Ribose 1,5-bisphosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,60030
Polymers218,7326
Non-polymers5,86824
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+y,y,-z+1/31
Buried area29780 Å2
ΔGint-126 kcal/mol
Surface area62980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.800, 98.800, 256.431
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

#1: Protein Ribose 1,5-bisphosphate isomerase


Mass: 36455.367 Da / Num. of mol.: 3 / Mutation: D204N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH0208 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)
References: UniProt: O57947, ribose-1,5-bisphosphate isomerase
#2: Sugar ChemComp-RI2 / 1,5-di-O-phosphono-alpha-D-ribofuranose / 1,5-di-O-phosphono-alpha-D-ribose / 1,5-di-O-phosphono-D-ribose / 1,5-di-O-phosphono-ribose


Type: D-saccharide, alpha linking / Mass: 310.090 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C5H12O11P2 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 310 molecules

#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 3.31 Å3/Da / Density % sol: 62.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.7 M NaCl, 3% PEG 6000, 20% MPD, 0.1% Low Melting Agarose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 21, 2017 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→85.56 Å / Num. obs: 53172 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.032 / Rrim(I) all: 0.113 / Net I/σ(I): 19.6 / Num. measured all: 671257 / Scaling rejects: 232
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
2.45-2.5315.10.575.246030.9670.1510.59
140.02383910.0070.024

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.54 Å85.56 Å
Translation5.54 Å85.56 Å

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOSFLM7.2.1data reduction
Aimless0.5.28data scaling
PHASER2.6.1phasing
REFMAC5.8.0155refinement
Coot0.8.6model building
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YFJ

5yfj


Resolution: 2.45→85.56 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.666 / SU ML: 0.171 / SU R Cruickshank DPI: 0.2808 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.281 / ESU R Free: 0.225
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 2618 4.9 %RANDOM
Rwork0.1675 ---
obs0.1704 50474 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 160.36 Å2 / Biso mean: 41.908 Å2 / Biso min: 17.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20.61 Å20 Å2
2--1.22 Å2-0 Å2
3----3.96 Å2
Refinement stepCycle: final / Resolution: 2.45→85.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7638 0 0 301 7939
Biso mean---38.33 -
Num. residues----978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0197988
X-RAY DIFFRACTIONr_bond_other_d0.0020.027826
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.97610843
X-RAY DIFFRACTIONr_angle_other_deg1.021318069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5145965
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.25824.209316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.614151453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2241545
X-RAY DIFFRACTIONr_chiral_restr0.0980.21232
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218615
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021659
LS refinement shellResolution: 2.45→2.514 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 175 -
Rwork0.234 3726 -
all-3901 -
obs--99.95 %

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