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

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Basic information

Entry
Database: PDB / ID: 5yfx
TitleCrystal structure of ribose-1,5-bisphosphate isomerase mutant D204N from Pyrococcus horikoshii OT3 in complex with ribose-1,5-bisphosphate and AMP
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 / pentose catabolic process / cellular biosynthetic process
Similarity search - Function
Ribose-1,5-bisphosphate isomerase, e2b2 family / Initiation factor 2B alpha/beta/delta / translation initiation factor eif-2b, domain 1 / Translation initiation factor eif-2b; domain 2 / Methylthioribose-1-phosphate isomerase, N-terminal / 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 / Translation initiation factor eif-2b; domain 2 / Methylthioribose-1-phosphate isomerase, N-terminal / 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
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: 2.7 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1133
Polymers36,4551
Non-polymers6572
Water81145
1
A: Ribose 1,5-bisphosphate isomerase
hetero molecules
x 6


  • defined by author&software
  • Evidence: -0.500000 -0.866025 0.000000 121.69500 0.866025 -0.500000 0.000000 70.26064 0.000000 0.000000 1.000000 0.00000 -0.500000 -0.866025 0.000000 121.69500 -0.866025 0.500000 0.000000 70.26064 0. ...Evidence: -0.500000 -0.866025 0.000000 121.69500 0.866025 -0.500000 0.000000 70.26064 0.000000 0.000000 1.000000 0.00000 -0.500000 -0.866025 0.000000 121.69500 -0.866025 0.500000 0.000000 70.26064 0.000000 0.000000 -1.000000 0.00000 -0.500000 0.866025 0.000000 0.00000 -0.866025 -0.500000 0.000000 140.52128 0.000000 0.000000 1.000000 0.00000 1.000000 0.000000 0.000000 0.00000 0.000000 -1.000000 0.000000 140.52128 0.000000 0.000000 -1.000000 0.00000
  • 223 kDa, 6 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)222,67618
Polymers218,7326
Non-polymers3,94412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_675x-y+1,-y+2,-z1
crystal symmetry operation6_765-x+2,-x+y+1,-z1
Buried area27040 Å2
ΔGint-96 kcal/mol
Surface area64020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.130, 81.130, 100.180
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-535-

HOH

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Components

#1: Protein Ribose 1,5-bisphosphate isomerase


Mass: 36455.367 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C5H12O11P2 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.61 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.7 M NaCl, 3% PEG 6000, 20% MPD

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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: Nov 23, 2016 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→100.18 Å / Num. obs: 10900 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.029 / Rrim(I) all: 0.094 / Net I/σ(I): 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.7-2.839.80.5414.414080.9520.1820.572100
9.10.0263550.9990.0090.02899.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.74 Å70.26 Å
Translation6.74 Å70.26 Å

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOSFLM7.2.1data processing
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: 2.7→100.18 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.884 / SU B: 14.891 / SU ML: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.366
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2644 552 5.1 %RANDOM
Rwork0.1765 ---
obs0.1809 10348 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 118.85 Å2 / Biso mean: 48.382 Å2 / Biso min: 12.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å2-0.93 Å2-0 Å2
2---1.85 Å20 Å2
3---6.02 Å2
Refinement stepCycle: final / Resolution: 2.7→100.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 41 45 2624
Biso mean--38.31 32.38 -
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192633
X-RAY DIFFRACTIONr_bond_other_d0.0020.022592
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.983570
X-RAY DIFFRACTIONr_angle_other_deg0.96135984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8755320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.62424.135104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.00215483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5811515
X-RAY DIFFRACTIONr_chiral_restr0.0850.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212847
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02547
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 21 -
Rwork0.285 758 -
all-779 -
obs--100 %

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