[English] 日本語
Yorodumi
- PDB-4em8: The Structure of Ribose 5-phosphate Isomerase B from Anaplasma ph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4em8
TitleThe Structure of Ribose 5-phosphate Isomerase B from Anaplasma phagocytophilum
ComponentsRibose 5-phosphate isomerase B
KeywordsISOMERASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology
Function and homology information


ribose-5-phosphate isomerase / ribose-5-phosphate 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 B
Similarity search - Component
Biological speciesAnaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: The Structure of Ribose 5-phosphate Isomerase B from Anaplasma phagocytophilum
Authors: Clifton, M.C. / Edwards, T.E. / Sankaran, B. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionApr 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,3932
Polymers32,3932
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-9 kcal/mol
Surface area11670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.360, 62.490, 73.960
Angle α, β, γ (deg.)90.000, 93.130, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ribose 5-phosphate isomerase B


Mass: 16196.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
Strain: HZ / Gene: rpiB, APH_0642 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2GK74, ribose-5-phosphate isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: AnphA.00455.a.A1 PW 35203 at 45.59 mg/mL, 200 mM potassium formate, 20% PEG3350, cryoprotectant: 20% ethylene glycol , pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 6, 2012
RadiationMonochromator: Asymmetric curved crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.95→35.307 Å / Num. obs: 23547 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 35.059 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 21.99
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.95-20.3993.988390171599.7
2-2.060.3275.168426169799.7
2.06-2.120.276.058327162399.8
2.12-2.180.2217.48367160399.9
2.18-2.250.1679.468287154899.9
2.25-2.330.14710.7581261494100
2.33-2.420.11613.497982144599.9
2.42-2.520.10315.177769139699.9
2.52-2.630.08218.427392132899.9
2.63-2.760.0721.327319130999.9
2.76-2.910.05426.3566291197100
2.91-3.080.04431.3763501160100
3.08-3.30.03538.3158961079100
3.3-3.560.03143.185475101499.8
3.56-3.90.02948.62502293999.9
3.9-4.360.02850.64443284099.8
4.36-5.030.02753.25382775199.2
5.03-6.170.02751.45340863599.5
6.17-8.720.02355.1269849399.6
8.720.02155.99145028198.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O1X

1o1x


Resolution: 1.95→35.307 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2124 / WRfactor Rwork: 0.1743 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.867 / SU B: 6.759 / SU ML: 0.096 / SU R Cruickshank DPI: 0.1517 / SU Rfree: 0.1418 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 1211 5.1 %RANDOM
Rwork0.1793 ---
obs0.1814 23534 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.12 Å2 / Biso mean: 30.7011 Å2 / Biso min: 18.49 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å20 Å2-0.44 Å2
2---0.91 Å20 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 1.95→35.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 0 136 2344
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.012
X-RAY DIFFRACTIONr_bond_other_d0.001
X-RAY DIFFRACTIONr_angle_refined_deg1.421
X-RAY DIFFRACTIONr_angle_other_deg0.949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.083
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.876
X-RAY DIFFRACTIONr_chiral_restr0.078
X-RAY DIFFRACTIONr_gen_planes_refined0.006
X-RAY DIFFRACTIONr_gen_planes_other
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 84 -
Rwork0.246 1575 -
all-1659 -
obs--99.7 %
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)
11.39420.97080.09864.5016-0.14541.796-0.0126-0.17750.02740.36510.00060.1193-0.2414-0.12910.0120.18830.02050.03140.136-0.01490.062111.36997.25835.7424
21.8503-1.66110.99728.7248-1.90254.0863-0.1003-0.14930.03140.42010.20080.45630.1821-0.6589-0.10050.0802-0.00860.07580.18750.02370.14712.9172-1.219532.1087
30.55370.20330.49492.0903-0.10612.1588-0.006-0.02040.0223-0.03530.01140.0955-0.0809-0.046-0.00540.10540.0070.01260.1161-0.00260.110210.63823.877621.8381
40.8245-0.08890.45721.8579-0.56113.34380-0.01650.0667-0.0120.05110.0134-0.28740.1025-0.05110.1044-0.00250.01730.09230.01270.095713.97848.753619.5476
520.7575-13.186517.030712.1529-11.503723.80970.09620.0495-0.3666-0.0937-0.03770.19830.48760.2035-0.05850.2999-0.060.00970.0198-0.01210.213911.2232-22.1828.1094
61.2279-0.8725-0.22042.39160.6331.7487-0.00240.1684-0.0154-0.3040.01630.12230.063-0.1536-0.01390.1527-0.0245-0.05030.11950.00030.094510.1489-7.6691.0868
70.7012-0.302-0.3161.72540.47581.9019-0.0195-0.03640.00380.04280.05060.01110.16510.016-0.03110.14150-0.0290.1110.00190.111812.8616-7.268213.4629
80.7956-0.3366-1.04780.91510.74323.4931-0.0613-0.0492-0.1370.16710.07490.01010.62860.0459-0.01360.2213-0.0023-0.02340.07070.04520.112912.7106-15.66119.4553
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 39
2X-RAY DIFFRACTION2A40 - 58
3X-RAY DIFFRACTION3A59 - 109
4X-RAY DIFFRACTION4A110 - 143
5X-RAY DIFFRACTION5B-1 - 4
6X-RAY DIFFRACTION6B5 - 58
7X-RAY DIFFRACTION7B59 - 115
8X-RAY DIFFRACTION8B116 - 142

+
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