[English] 日本語
Yorodumi
- PDB-4io1: Crystal structure of ribose-5-isomerase A from Francisella Tularensis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4io1
TitleCrystal structure of ribose-5-isomerase A from Francisella Tularensis
ComponentsRibose-5-phosphate isomerase A
KeywordsISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch
Similarity search - Function
Ribose-5-phosphate isomerase, type A, subgroup / Ribose 5-phosphate isomerase, type A / Ribose 5-phosphate isomerase A (phosphoriboisomerase A) / Rossmann fold - #1360 / ACT domain / NagB/RpiA transferase-like / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / PHOSPHATE ION / Ribose-5-phosphate isomerase A
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRostankowski, R. / Nakka, C. / Grimshaw, S. / Borek, D. / Otwinowski, Z. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be published
Title: Structural and biophysical studies of Ribose-5-Phosphate Isomerase A from Francisella Tularensis
Authors: Rostankowski, R. / Orlikowska, M. / Nakka, C. / Grimshaw, S. / Borek, D. / Otwinowski, Z. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,84014
Polymers48,9882
Non-polymers85212
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-87 kcal/mol
Surface area18020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.281, 85.765, 70.634
Angle α, β, γ (deg.)90.00, 94.52, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Ribose-5-phosphate isomerase A / Phosphoriboisomerase A / PRI


Mass: 24494.209 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: FTT_1208, FTW_1255, rpiA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q5NFM5, ribose-5-phosphate isomerase

-
Non-polymers , 5 types, 275 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Sodium Bromide, 0.1M Bis-Tris propane pH 6.5 20% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 51768 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.067
Reflection shellResolution: 1.65→1.68 Å / % possible all: 98.5

-
Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
REFMAC5.5.0066refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3KWM
Resolution: 1.65→36.63 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.355 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18207 2602 5.1 %RANDOM
Rwork0.14781 ---
obs0.14962 48581 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.123 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å2-0.25 Å2
2---0.03 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.65→36.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3299 0 36 263 3598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223484
X-RAY DIFFRACTIONr_bond_other_d00.023284
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9914736
X-RAY DIFFRACTIONr_angle_other_deg0.66237690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0725458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.51326.277137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64715649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.1431513
X-RAY DIFFRACTIONr_chiral_restr0.0850.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023871
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02602
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5281.52228
X-RAY DIFFRACTIONr_mcbond_other0.9921.5918
X-RAY DIFFRACTIONr_mcangle_it3.88223640
X-RAY DIFFRACTIONr_scbond_it5.9631256
X-RAY DIFFRACTIONr_scangle_it9.1494.51096
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 166 -
Rwork0.231 3396 -
obs--94.94 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
110.5516-5.4483-1.33633.59243.661114.6270.01180.43580.5318-0.1414-0.19780.0257-0.7446-0.71960.1860.14030.0774-0.00980.20010.23510.4045-2.49211.90512.21
21.891-0.22990.52238.61990.85661.2524-0.1150.41220.0764-0.45590.24910.1803-0.0402-0.0573-0.13410.1112-0.0202-0.00250.19780.05070.04781.618-1.24410.196
31.4407-1.91230.36073.3246-0.03720.81050.0510.0993-0.0083-0.03350.00260.08020.1537-0.1387-0.05360.084-0.04290.00140.17310.03350.06621.537-8.99119.366
42.17710.75460.79513.39392.0451.3022-0.05150.33720.18440.0134-0.06380.15120.011-0.00760.11530.0671-0.0032-0.00690.15510.02190.0183-4.499-4.68115.248
50.9044-1.08810.65521.79341.30799.88130.13910.0189-0.1279-0.1464-0.08910.14840.2837-0.3979-0.04990.0652-0.0415-0.00650.0575-0.02390.0335-1.604-15.49118.39
63.0634-0.47110.17190.7756-0.54122.0835-0.06670.045-0.0610.06550.05190.0380.0082-0.17810.01480.02090.00420.01790.0863-0.00590.0172-6.821-5.54425.738
73.1158-2.90332.6952.9062-3.01186.95650.2455-0.2794-0.1956-0.16840.22010.14470.5241-0.4936-0.46560.1196-0.0933-0.05520.09380.04140.1022-0.258-15.8929.433
80.7580.83220.2713.78460.68371.49260.02380.1415-0.05610.0455-0.0541-0.08130.122-0.18250.03030.0520.00150.02440.0868-0.01860.02866.769-8.21321.449
910.7014-7.844-2.89176.59230.22085.49390.14020.28710.5291-0.0578-0.1744-0.4784-0.3240.01750.03420.1115-0.04740.03890.09740.01890.0617.8276.56318.764
100.82250.44030.07671.1182-0.07171.23890.04410.0404-0.01730.0281-0.0138-0.0313-0.0403-0.1041-0.03030.03250.01460.01920.04850.00280.01569.969-1.77227.592
110.7501-0.58410.041410.2913-0.61561.84620.00690.1828-0.0572-0.1636-0.1503-0.06250.043-0.08060.14340.03510.00950.02760.0733-0.02230.037410.732-7.69917.546
126.02991.81542.49851.90151.28581.6068-0.18480.28010.3051-0.20390.12820.0231-0.24230.04690.05660.09590.0170.02210.0450.02630.027911.8059.05717.396
130.221-0.2211-0.24671.6177-0.80991.2414-0.0274-0.01650.00290.157-0.0115-0.0394-0.1704-0.05780.03890.09270.04130.0030.0631-0.01490.021212.1837.34441.28
1410.31073.38432.30524.9657-1.10932.1972-0.12470.13830.33080.4129-0.0967-0.0086-0.49870.06750.22140.1619-0.0071-0.03460.0313-0.00660.03712.98912.84440.19
152.53162.55850.00583.5488-0.74871.01620.0034-0.10210.08290.1284-0.03660.046-0.1823-0.19980.03320.07910.03840.02670.0654-0.01180.03096.6527.36937.827
165.0933-2.8865-1.26939.4096.0854.02420.14430.16170.3942-0.55410.1089-0.4694-0.36140.0987-0.25320.0614-0.0010.04370.04340.01780.064723.7937.08328.926
172.2804-2.17171.36243.3728-1.87023.2979-0.0689-0.03460.11250.10660.0092-0.1313-0.08990.05190.05980.0310.00490.01580.0207-0.0020.021421.4341.22836.344
180.69640.07910.02820.45070.77931.43420.02340.0359-0.0641-0.00690.029-0.06580.01390.0108-0.05250.0490.02440.03340.0591-0.01210.054515.694-0.81729.602
195.4587-4.15911.200613.0069-3.54493.1703-0.01210.29030.2218-0.4060.18590.4537-0.11050.1112-0.17380.0673-0.008-0.01330.08130.04240.05237.1498.1678.417
201.4816-1.04412.527412.8162-3.34424.5185-0.15450.31770.2371-0.4262-0.2711-0.3861-0.20640.52460.42560.11580.03170.01420.18220.07380.052910.0214.1757.107
210.50091.17320.60662.79031.63471.8210.17910.05250.19860.48820.12390.36460.50420.0273-0.3030.26470.0179-0.01860.27650.14330.404321.944-12.3473.963
222.0504-4.73320.977812.7319-0.98341.4501-0.3631-0.31050.20930.4830.457-0.6721-0.3861-0.2196-0.09390.15930.0978-0.02930.2182-0.05590.080424.1440.08571.497
232.8647-1.14490.988610.26173.79242.83310.1201-0.54860.24690.4595-0.3710.26240.001-0.5260.2510.19010.00190.0280.2021-0.07130.055617.3995.57465.247
2410.5596-2.8037-5.72142.54562.76715.0413-0.4833-1.0282-1.43270.16540.09510.0010.2713-0.05840.38820.12540.06430.06310.43030.20770.296814.831-6.1469.674
259.3692-2.4-0.51117.8186-2.56674.76540.0618-1.09890.48580.43610.41710.1762-0.49320.4651-0.47890.20250.04490.02220.3472-0.14280.084315.8535.82473.696
2610.0198-0.4155-2.79951.6713-0.73893.6672-0.26620.1821-0.52560.2125-0.04720.2121-0.1226-0.82040.31340.12240.02880.06740.3107-0.07910.10697.651-1.0765.031
270.86410.5149-0.91220.37010.349913.65970.14710.08060.10270.08380.04930.0538-0.2186-0.2069-0.19640.06420.06550.01910.1315-0.00660.01947.1134.70663.929
2810.8839-0.43516.39561.9136-0.20614.0669-0.51210.06260.46370.17790.138-0.0689-0.25770.03870.37410.11920.02980.00750.057-0.02130.076711.258.81355.124
291.0072-0.6769-0.53412.00111.35111.8395-0.0308-0.10550.06060.1946-0.0362-0.05220.0517-0.03160.06690.0413-0.0061-0.00680.0564-0.00390.018222.594-5.76758.899
300.3233-0.51710.32821.1501-0.17490.8067-0.021-0.0391-0.00480.07380.0080.0355-0.044-0.06410.0130.0473-0.010.01710.07770.00110.007918.986-6.31752.906
312.6205-2.14123.15659.1244-4.24024.91030.1051-0.21070.00340.24930.0384-0.17480.1128-0.0726-0.14340.06410.002-0.00420.1036-0.02630.060125.003-5.2961.812
322.8661-1.05880.9056.04271.11941.86050.1657-0.0567-0.47380.4519-0.0437-0.72370.3483-0.0288-0.1220.1374-0.0031-0.07710.09130.03440.277428.454-18.02655.038
330.7911-0.46230.66450.79580.02791.66990.0861-0.0313-0.0385-0.0433-0.00570.04210.0733-0.0897-0.08040.0381-0.01090.01440.01660.0070.024612.545-14.69939.407
343.9399-1.4443-1.90292.9378-0.26044.14840.0914-0.03080.0613-0.08980.0935-0.0680.40790.0246-0.1850.0866-0.0151-0.01180.0245-0.01140.039316.32-20.14339.959
355.57942.6139-0.65584.7461-2.06220.95720.1835-0.3206-0.05690.0784-0.15630.1002-0.00180.0323-0.02720.0879-0.01710.07750.13210.010.08293.785-13.648.514
365.2815-4.57340.92154.48740.35572.71050.2726-0.1542-0.1275-0.21040.00040.00890.0985-0.278-0.2730.0585-0.02490.01950.06860.00910.053310.786-15.12444.324
3710.87055.83870.04974.3381-1.18522.4063-0.11940.4096-0.117-0.02250.1397-0.03630.21360.2769-0.02030.09240.02280.00210.0618-0.0090.021725.024-20.73944.81
387.8781-0.38324.887810.0289-5.7856.10720.23260.3404-0.0676-0.2047-0.4867-0.52950.24650.47640.25410.0350.02040.03020.08990.0290.051330.046-10.72343.163
391.56030.65060.48290.4954-0.34041.80150.06360.02060.047-0.0175-0.04070.02210.08780.0932-0.02290.03670.0090.02010.0442-0.00290.015320.394-7.82741.739
400.6626-2.081.73557.129-6.362210.288-0.055-0.06280.12450.14940.1221-0.39080.25250.182-0.06710.03880.0145-0.04520.0928-0.02230.060729.949-9.70364.97
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 11
2X-RAY DIFFRACTION2A12 - 25
3X-RAY DIFFRACTION3A26 - 36
4X-RAY DIFFRACTION4A37 - 49
5X-RAY DIFFRACTION5A50 - 56
6X-RAY DIFFRACTION6A57 - 71
7X-RAY DIFFRACTION7A72 - 78
8X-RAY DIFFRACTION8A79 - 90
9X-RAY DIFFRACTION9A91 - 95
10X-RAY DIFFRACTION10A96 - 116
11X-RAY DIFFRACTION11A117 - 121
12X-RAY DIFFRACTION12A122 - 132
13X-RAY DIFFRACTION13A133 - 152
14X-RAY DIFFRACTION14A153 - 164
15X-RAY DIFFRACTION15A165 - 180
16X-RAY DIFFRACTION16A181 - 188
17X-RAY DIFFRACTION17A189 - 194
18X-RAY DIFFRACTION18A195 - 212
19X-RAY DIFFRACTION19A213 - 218
20X-RAY DIFFRACTION20A219 - 224
21X-RAY DIFFRACTION21B10 - 17
22X-RAY DIFFRACTION22B18 - 25
23X-RAY DIFFRACTION23B26 - 33
24X-RAY DIFFRACTION24B34 - 46
25X-RAY DIFFRACTION25B47 - 52
26X-RAY DIFFRACTION26B53 - 70
27X-RAY DIFFRACTION27B71 - 75
28X-RAY DIFFRACTION28B76 - 81
29X-RAY DIFFRACTION29B82 - 94
30X-RAY DIFFRACTION30B95 - 116
31X-RAY DIFFRACTION31B117 - 125
32X-RAY DIFFRACTION32B126 - 134
33X-RAY DIFFRACTION33B135 - 152
34X-RAY DIFFRACTION34B153 - 163
35X-RAY DIFFRACTION35B164 - 170
36X-RAY DIFFRACTION36B171 - 177
37X-RAY DIFFRACTION37B178 - 182
38X-RAY DIFFRACTION38B183 - 188
39X-RAY DIFFRACTION39B189 - 206
40X-RAY DIFFRACTION40B207 - 224

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more