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- PDB-3s5p: Crystal structure of ribose-5-phosphate isomerase B RpiB from Gia... -

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Basic information

Entry
Database: PDB / ID: 3s5p
TitleCrystal structure of ribose-5-phosphate isomerase B RpiB from Giardia lamblia
ComponentsRibose 5-phosphate isomerase
KeywordsISOMERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Giardia / ribose-5-phosphate / ribulose-5-phosphate / RpiB / RpiA / pentose phosphate pathway / pentose-phosphate shunt / flagellated protozoan parasite / gastrointestinal tract parasite
Function / homology
Function and homology information


ribose-5-phosphate isomerase activity / isomerase activity / carbohydrate metabolic process
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
Similarity search - Component
Biological speciesGiardia lamblia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of ribose-5-phosphate isomerase B RpiB from Giardia lamblia
Authors: Edwards, T.E. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMay 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Ribose 5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7987
Polymers35,3182
Non-polymers4805
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-78 kcal/mol
Surface area11090 Å2
MethodPISA
2
B: Ribose 5-phosphate isomerase
hetero molecules

A: Ribose 5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7987
Polymers35,3182
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_444-x+y-1,-x-1,z-1/31
Buried area2310 Å2
ΔGint-74 kcal/mol
Surface area11410 Å2
MethodPISA
3
A: Ribose 5-phosphate isomerase
B: Ribose 5-phosphate isomerase
hetero molecules

A: Ribose 5-phosphate isomerase
B: Ribose 5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,59714
Polymers70,6364
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area7630 Å2
ΔGint-169 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.200, 89.200, 68.240
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-176-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 4 / Auth seq-ID: 1 - 128 / Label seq-ID: 22 - 149

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Ribose 5-phosphate isomerase


Mass: 17658.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia lamblia (eukaryote) / Strain: ATCC 50803 WB C6 / Gene: GL50803_27614 / Production host: Escherichia coli (E. coli) / References: UniProt: A8B2K2, ribose-5-phosphate isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: GilaA.01163.a.A1 PS00138 at 24 mg/mL with 5 mM ribose-5-phosphate against JCSG+ screen condition A6 0.2 M Li2SO4, 0.1 M phosphate/citrate pH 4.2, 20% PEG 1000, crystal tracking ID 215117a6, ...Details: GilaA.01163.a.A1 PS00138 at 24 mg/mL with 5 mM ribose-5-phosphate against JCSG+ screen condition A6 0.2 M Li2SO4, 0.1 M phosphate/citrate pH 4.2, 20% PEG 1000, crystal tracking ID 215117a6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. all: 14267 / Num. obs: 13930 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 55.729 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 22.39
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.3-2.360.5352.533339100396.3
2.36-2.420.4553.1336921002100
2.42-2.490.3613.9366698599.3
2.49-2.570.2555.5347594298.9
2.57-2.660.1877.33339891999
2.66-2.750.1628.25328688799
2.75-2.850.11411.29321186698.7
2.85-2.970.09513.36314884798.8
2.97-3.10.07117.46289477898.4
3.1-3.250.04824.36281576398.5
3.25-3.430.03532.1268672398.2
3.43-3.640.02739.18253368498.1
3.64-3.890.02444.46242365698.1
3.89-4.20.02347.79212457797
4.2-4.60.02152.5201253993.6
4.6-5.140.0251.85181650296.2
5.14-5.940.02450.39157743494.3
5.94-7.270.0252.5132637193.9
7.27-10.290.01460.9105129592.5
10.290.01660.451615784

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2vvr

2vvr


Resolution: 2.3→38.62 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2291 / WRfactor Rwork: 0.1905 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8451 / SU B: 13.011 / SU ML: 0.15 / SU R Cruickshank DPI: 0.272 / SU Rfree: 0.2098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 701 5.1 %RANDOM
Rwork0.1982 ---
obs0.2 13881 97.31 %-
all-14267 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 127.66 Å2 / Biso mean: 50.4842 Å2 / Biso min: 7.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å20 Å2
2--0.46 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 25 50 1885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211861
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9552510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7195257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.83122.64768
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99615274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0571515
X-RAY DIFFRACTIONr_chiral_restr0.0860.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021377
X-RAY DIFFRACTIONr_mcbond_it0.8331.51270
X-RAY DIFFRACTIONr_mcangle_it1.55221971
X-RAY DIFFRACTIONr_scbond_it2.2843591
X-RAY DIFFRACTIONr_scangle_it3.5634.5538
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 821 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.220.5
MEDIUM THERMAL0.942
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 58 -
Rwork0.3 937 -
all-995 -
obs--96.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.55131.36571.76213.2599-1.152711.65210.3564-0.47260.50820.8151-0.2839-0.0379-2.0210.6948-0.07250.6644-0.20260.12270.2577-0.13410.338-47.64268.65145.7593
24.0468-4.11620.798511.149-4.92359.42260.2996-0.02580.54581.0793-0.07420.3576-0.88220.3101-0.22540.4002-0.08540.23130.2087-0.14290.296-51.27962.627910.7068
32.10070.02330.83132.8458-0.94452.7020.1338-0.09220.04180.285-0.1637-0.0717-0.18130.29040.02990.2834-0.10750.05020.127-0.1090.1677-42.594-4.8514.3504
41.84661.7417-0.61894.2501-1.96663.70230.09910.00180.05650.0497-0.09410.2451-0.1212-0.0319-0.0050.191-0.03640.06320.0666-0.10140.1763-49.6712-2.4386-2.1034
54.21250.0375-0.89962.8756-0.16953.69810.18760.2393-0.0424-0.142-0.06240.03240.2095-0.0826-0.12520.2190.1018-0.02820.113-0.03750.1379-32.0348-19.4149-12.2121
62.9286-1.8023-1.20476.17334.50358.39890.3781-0.1727-0.12630.952-0.11320.03161.36450.4069-0.2650.44710.0556-0.0850.21040.01470.1554-28.6675-21.9418-3.4576
71.0298-0.7392-0.69131.0318-0.05532.9670.0676-0.10870.05110.2299-0.0678-0.05190.110.3650.00020.2866-0.0153-0.01680.1724-0.06820.1635-33.9873-10.2041-0.4685
82.6753-1.3270.41762.4366-0.34265.75710.2509-0.0390.1730.0789-0.1628-0.2519-0.06670.4319-0.08810.2070.014-0.01110.1399-0.04970.1838-29.2934-7.8979-5.4638
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 20
2X-RAY DIFFRACTION2A21 - 60
3X-RAY DIFFRACTION3A61 - 90
4X-RAY DIFFRACTION4A91 - 128
5X-RAY DIFFRACTION5B1 - 21
6X-RAY DIFFRACTION6B22 - 58
7X-RAY DIFFRACTION7B59 - 97
8X-RAY DIFFRACTION8B98 - 129

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