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- PDB-6mu0: Crystal Structure of Ribose-5-phosphate Isomerase B from Mycoplas... -

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Basic information

Entry
Database: PDB / ID: 6mu0
TitleCrystal Structure of Ribose-5-phosphate Isomerase B from Mycoplasma genitalium with bound Ribulose-5-phosphate
ComponentsProbable ribose-5-phosphate isomerase B
KeywordsISOMERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


D-allose catabolic process / ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch / isomerase activity
Similarity search - Function
Ribose 5-phosphate isomerase B / Sugar-phosphate isomerase, RpiB/LacA/LacB family / Sugar-phosphate isomerase, RpiB/LacA/LacB superfamily / Ribose/Galactose Isomerase / Ribose 5-phosphate Isomerase B; Chain: A, / Sugar-phosphate isomerase, RpiB/LacA/LacB / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RIBULOSE-5-PHOSPHATE / Probable ribose-5-phosphate isomerase B
Similarity search - Component
Biological speciesMycoplasma genitalium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Ribose-5-phosphate Isomerase B from Mycoplasma genitalium with bound Ribulose-5-phosphate
Authors: Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionOct 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

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Assembly

Deposited unit
A: Probable ribose-5-phosphate isomerase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2122
Polymers17,9821
Non-polymers2301
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Probable ribose-5-phosphate isomerase B
hetero molecules

A: Probable ribose-5-phosphate isomerase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4234
Polymers35,9632
Non-polymers4602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area4520 Å2
ΔGint-10 kcal/mol
Surface area12360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.350, 45.350, 138.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Probable ribose-5-phosphate isomerase B / Phosphoriboisomerase B


Mass: 17981.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195) (bacteria)
Strain: ATCC 33530 / G-37 / NCTC 10195 / Gene: rpiB, MG396 / Plasmid: MygeA.00966.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P47636, ribose-5-phosphate isomerase
#2: Sugar ChemComp-5RP / RIBULOSE-5-PHOSPHATE


Type: saccharide / Mass: 230.110 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 1.98 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: MygeA.00966.a.B1.PW38486 at 15.59 mg/ml was incubated with 5 mM ribose-5-phosphate, then was mixed 1:1 JCSG+(d5): 70% (v/v) MPD 0.1 M HEPES free acid, pH 7.0, Tray: 302126d5, puck: ppf0-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 16, 2018 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.1→43.099 Å / Num. obs: 59627 / % possible obs: 99.7 % / Redundancy: 9.053 % / Biso Wilson estimate: 13.828 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.118 / Χ2: 0.961 / Net I/σ(I): 11.67 / Num. measured all: 539804 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.137.0090.5183.2329614434842250.870.55997.2
1.13-1.168.8730.4184.5737470422442230.9290.444100
1.16-1.199.1790.3355.7238150415741560.9570.355100
1.19-1.239.2430.2956.5736832398539850.9620.312100
1.23-1.279.2860.2567.536011387838780.9720.271100
1.27-1.319.310.2248.4834932375737520.9780.23799.9
1.31-1.369.2940.1989.5733969365836550.9820.2199.9
1.36-1.429.3110.17910.6532672351535090.9820.1999.8
1.42-1.489.3670.15912.0531361335133480.9860.16899.9
1.48-1.569.2940.13513.7730167324832460.990.14399.9
1.56-1.649.2650.12715.0328517308430780.9890.13499.8
1.64-1.749.2550.1216.0927137293529320.9890.12699.9
1.74-1.869.290.11417.3425445274527390.990.1299.8
1.86-2.019.2010.10618.4623749258225810.9910.112100
2.01-2.29.2550.10319.4122175239823960.9910.10999.9
2.2-2.469.2640.10119.8820186217921790.9920.106100
2.46-2.849.2580.09820.2717989194319430.9910.103100
2.84-3.489.1890.09920.5415428167916790.9880.105100
3.48-4.928.8560.09920.4711743132613260.9920.105100
4.92-43.0997.8510.09619.0262578027970.9870.10399.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_3283)refinement
PDB_EXTRACT3.24data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HE8

3he8


Resolution: 1.1→43.099 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 11.81
RfactorNum. reflection% reflection
Rfree0.1487 3557 6.15 %
Rwork0.1337 --
obs0.1346 57876 96.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.01 Å2 / Biso mean: 15.0653 Å2 / Biso min: 6.63 Å2
Refinement stepCycle: final / Resolution: 1.1→43.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1174 0 14 219 1407
Biso mean--9.8 28.93 -
Num. residues----152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051252
X-RAY DIFFRACTIONf_angle_d0.9331701
X-RAY DIFFRACTIONf_dihedral_angle_d18.876473
X-RAY DIFFRACTIONf_chiral_restr0.079200
X-RAY DIFFRACTIONf_plane_restr0.004218
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.11510.16921300.16251873200386
1.1151-1.1310.19681320.15181998213090
1.131-1.14790.15471320.15012040217293
1.1479-1.16590.18221550.13822084223994
1.1659-1.1850.15051310.13122076220795
1.185-1.20540.15641230.12962094221795
1.2054-1.22730.151400.12142112225296
1.2273-1.25090.12351340.11912127226196
1.2509-1.27650.14711620.11932093225596
1.2765-1.30420.14291180.11782193231198
1.3042-1.33460.15391350.11542183231897
1.3346-1.3680.1431380.11562139227797
1.368-1.40490.12961430.11712162230598
1.4049-1.44630.1291430.11272174231798
1.4463-1.4930.16771420.11262210235298
1.493-1.54630.12261500.11032180233098
1.5463-1.60830.12431630.11072199236299
1.6083-1.68140.12131190.11732244236399
1.6814-1.77010.15131370.12982222235999
1.7701-1.8810.14811520.13792253240599
1.881-2.02620.13921610.12922412402100
2.0262-2.23010.15181710.135422452416100
2.2301-2.55280.12661460.139623272473100
2.5528-3.21610.14881550.142423352490100
3.2161-43.13180.17691450.149925152660100

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