[English] 日本語
Yorodumi
- PDB-2ppw: The crystal structure of uncharacterized Ribose 5-phosphate isome... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ppw
TitleThe crystal structure of uncharacterized Ribose 5-phosphate isomerase RpiB from Streptococcus pneumoniae
ComponentsConserved domain protein
KeywordsISOMERASE / The putative RpiB / Streptococcus pneumoniae / PSI-2 / Protein Structure Initiative / MCSG / Structural Genomics / Midwest Center for Structural Genomics
Function / homology
Function and homology information


lactose metabolic process / intramolecular oxidoreductase activity, interconverting aldoses and ketoses / isomerase activity
Similarity search - Function
Ribose-5-phosphate isomerase, C-terminal / Ribose-5-phosphate isomerase / 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
Conserved domain protein / Conserved domain protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsWu, R. / Zhang, R. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of uncharacterized Ribose 5-phosphate isomerase RpiB from Streptococcus pneumoniae.
Authors: Wu, R. / Zhang, R. / Abdullah, J. / Joachimiak, A.
History
DepositionApr 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Conserved domain protein
B: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7934
Polymers48,6012
Non-polymers1922
Water4,882271
1
A: Conserved domain protein
hetero molecules

A: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7934
Polymers48,6012
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area3790 Å2
ΔGint-56 kcal/mol
Surface area17420 Å2
MethodPISA
2
B: Conserved domain protein
hetero molecules

B: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7934
Polymers48,6012
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area3690 Å2
ΔGint-59 kcal/mol
Surface area17140 Å2
MethodPISA
3
A: Conserved domain protein
B: Conserved domain protein
hetero molecules

A: Conserved domain protein
B: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5868
Polymers97,2024
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area11260 Å2
ΔGint-146 kcal/mol
Surface area30790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.915, 52.416, 85.018
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Conserved domain protein / Uncharacterized ribose 5-phosphate isomerase RpiB


Mass: 24300.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_0319 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q97SL3, UniProt: A0A0H2UNJ8*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Na acetate pH 4.6, 0.4M Mg formate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2007 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.01→85.13 Å / Num. all: 27060 / Num. obs: 26774 / % possible obs: 99.5 % / Redundancy: 9.3 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 21.86
Reflection shellResolution: 2.01→2.07 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1873 / % possible all: 91.46

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→85.13 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.137 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.195 / ESU R Free: 0.164
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21807 1421 5 %RANDOM
Rwork0.17691 ---
obs0.17902 26774 98.94 %-
all-26774 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.135 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.01→85.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3269 0 10 271 3550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223379
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.9674565
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9495427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.87725.346159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59215593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6831513
X-RAY DIFFRACTIONr_chiral_restr0.0870.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022569
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.21618
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22355
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2251
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.2100
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.771.52197
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10323345
X-RAY DIFFRACTIONr_scbond_it1.97331395
X-RAY DIFFRACTIONr_scangle_it3.0224.51220
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 79 -
Rwork0.189 1794 -
obs-1873 91.46 %
Refinement TLS params.Method: refined / Origin x: 82.924 Å / Origin y: -0.117 Å / Origin z: 57.92 Å
111213212223313233
T-0.0868 Å20.0291 Å20.0158 Å2--0.0523 Å20.0151 Å2---0.0482 Å2
L0.5732 °2-0.1877 °20.0992 °2-0.4178 °20.1403 °2--1.3117 °2
S-0.0938 Å °-0.1298 Å °-0.0219 Å °0.097 Å °0.0856 Å °0.0531 Å °0.0043 Å °-0.1643 Å °0.0083 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 504 - 53
2X-RAY DIFFRACTION1AA51 - 10054 - 103
3X-RAY DIFFRACTION1AA101 - 150104 - 153
4X-RAY DIFFRACTION1AA151 - 209154 - 212
5X-RAY DIFFRACTION1BB1 - 504 - 53
6X-RAY DIFFRACTION1BB51 - 10054 - 103
7X-RAY DIFFRACTION1BB101 - 150104 - 153
8X-RAY DIFFRACTION1BB151 - 208154 - 211

+
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://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