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- PDB-1nn4: Structural Genomics, RpiB/AlsB -

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Basic information

Entry
Database: PDB / ID: 1nn4
TitleStructural Genomics, RpiB/AlsB
ComponentsRibose 5-phosphate isomerase B
KeywordsISOMERASE / Structural Genomics / alpha/beta/alpha sandwich / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


D-allose 6-phosphate isomerase activity / D-allose catabolic process / ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch
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
Ribose-5-phosphate isomerase B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsZhang, R.G. / Andersson, C.E. / Mowbray, S.L. / Savchenko, A. / Skarina, T. / Evdokimova, E. / Beasley, S.L. / Arrowsmith, C. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The 2.2 A resolution structure of RpiB/AlsB from Escherichia coli illustrates a new approach to the ribose-5-phosphate isomerase reaction.
Authors: Zhang, R.G. / Andersson, C.E. / Skarina, T. / Evdokimova, E. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Mowbray, S.L.
History
DepositionJan 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribose 5-phosphate isomerase B
B: Ribose 5-phosphate isomerase B
C: Ribose 5-phosphate isomerase B
D: Ribose 5-phosphate isomerase B


Theoretical massNumber of molelcules
Total (without water)69,9234
Polymers69,9234
Non-polymers00
Water5,368298
1
A: Ribose 5-phosphate isomerase B
D: Ribose 5-phosphate isomerase B


Theoretical massNumber of molelcules
Total (without water)34,9622
Polymers34,9622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-16 kcal/mol
Surface area13610 Å2
MethodPISA
2
B: Ribose 5-phosphate isomerase B
C: Ribose 5-phosphate isomerase B


Theoretical massNumber of molelcules
Total (without water)34,9622
Polymers34,9622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-16 kcal/mol
Surface area13400 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11740 Å2
ΔGint-59 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.588, 145.588, 74.784
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
DetailsThere are 4 monomers (two dimers) in asymmetric unit. The biological assembly of two dimers are generated by Chains A/D, and B/C.

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Components

#1: Protein
Ribose 5-phosphate isomerase B / Phosphoriboisomerase B / RPIB/ALSB


Mass: 17480.795 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: RPIB / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P37351, ribose-5-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.83 Å3/Da / Density % sol: 56.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 3M Na Acetate, 4% Ethylene Glycol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 7.5 / PH range high: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 M1reservoirNaCl
20.05 MHEPES1reservoirpH6.8-7.5
350 mMTris-HCl1droppH7.8
4150 mM1dropNaCl
55 mMMESNA1drop
621 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795, 0.9797, 0.94656
DetectorType: SBC-2 / Detector: CCD / Date: Feb 10, 2002 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97971
30.946561
ReflectionResolution: 2.2→50 Å / Num. all: 39615 / Num. obs: 38823 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 6.83 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 18.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3 / Num. unique all: 3858 / % possible all: 97.9
Reflection
*PLUS
Num. measured all: 265246

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Processing

Software
NameVersionClassification
CNS0.9refinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→36.4 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The number of reflections for refinement is greater than the number of reflections for data collection, because in CNS (hlml taget) refinement, the Friedel's pair was treated as two seperated reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3432 4.9 %RANDOM
Rwork0.216 ---
obs0.217 69714 89.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.2991 Å2 / ksol: 0.363482 e/Å3
Displacement parametersBiso mean: 40.5 Å2
Baniso -1Baniso -2Baniso -3
1--12.82 Å20 Å20 Å2
2---12.82 Å20 Å2
3---25.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.2→36.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4763 0 0 298 5061
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it3.052.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 472 4.7 %
Rwork0.372 9657 -
obs--77.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 36.4 Å / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shell
*PLUS
Rfactor Rfree: 0.381 / Rfactor Rwork: 0.373

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