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- PDB-5yfu: Crystal structure of ribose-1,5-bisphosphate isomerase from Pyroc... -

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Basic information

Entry
Database: PDB / ID: 5yfu
TitleCrystal structure of ribose-1,5-bisphosphate isomerase from Pyrococcus horikoshii OT3 in complex with ribulose-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 / 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
ADENOSINE MONOPHOSPHATE / : / RIBULOSE-1,5-DIPHOSPHATE / Ribose 1,5-bisphosphate isomerase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 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 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
B: Ribose-1,5-bisphosphate isomerase
C: Ribose-1,5-bisphosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,57613
Polymers109,3693
Non-polymers2,20710
Water5,783321
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)223,15326
Polymers218,7386
Non-polymers4,41520
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_657-x+y+1,y,-z+7/31
Buried area32970 Å2
ΔGint-170 kcal/mol
Surface area62840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.980, 98.980, 256.611
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-583-

HOH

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

#1: Protein Ribose-1,5-bisphosphate isomerase


Mass: 36456.352 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT3
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-RUB / RIBULOSE-1,5-DIPHOSPHATE


Type: saccharide / Mass: 310.090 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C5H12O11P2 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 328 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 3.32 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.7 M NaCl, 3% PEG 6000, 25% 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 9, 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: 2.35→85.72 Å / Num. obs: 60380 / % possible obs: 100 % / Redundancy: 11 % / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.036 / Rrim(I) all: 0.12 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.35-2.4111.30.5853.744250.9720.1830.614100
10.20.0397520.9970.0130.04299.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.54 Å81.3 Å
Translation5.54 Å81.3 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: 2.35→85.72 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.989 / SU ML: 0.18 / SU R Cruickshank DPI: 0.2471 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.224
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 3075 5.1 %RANDOM
Rwork0.1801 ---
obs0.1836 57076 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 121.93 Å2 / Biso mean: 47.803 Å2 / Biso min: 23.33 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20.7 Å20 Å2
2--1.4 Å2-0 Å2
3----4.54 Å2
Refinement stepCycle: final / Resolution: 2.35→85.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7638 0 134 321 8093
Biso mean--41.86 42.08 -
Num. residues----966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0197940
X-RAY DIFFRACTIONr_bond_other_d0.0020.027812
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.9810764
X-RAY DIFFRACTIONr_angle_other_deg1.022318039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7445967
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.35624.209316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.515151457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2541545
X-RAY DIFFRACTIONr_chiral_restr0.0960.21219
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218600
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021642
LS refinement shellResolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 222 -
Rwork0.267 4185 -
all-4407 -
obs--99.71 %

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