[English] 日本語
Yorodumi
- PDB-6mc0: Crystal Structure of Ribose-5-phosphate Isomerase from Legionella... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mc0
TitleCrystal Structure of Ribose-5-phosphate Isomerase from Legionella pneumophila with Bound Substrate Ribose-5-Phosphate and Product Ribulose-5-Phosphate
ComponentsRibose-5-phosphate isomerase A
KeywordsISOMERASE / SSGCID / pentose phosphate pathway / ribose-5-phosphate / ribulose-5-phosphate / Ribose-5-phosphate Isomerase / carbohydrate degradation / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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
RIBULOSE-5-PHOSPHATE / RIBOSE-5-PHOSPHATE / Ribose-5-phosphate isomerase A
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Ribose-5-phosphate Isomerase from Legionella pneumophila with Bound Substrate Ribose-5-Phosphate and Product Ribulose-5-Phosphate
Authors: Braverman, K.N. / Dranow, D.M. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionAug 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)48,6606
Polymers48,1542
Non-polymers5064
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-37 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.290, 67.560, 73.320
Angle α, β, γ (deg.)90.000, 118.820, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-602-

HOH

-
Components

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


Mass: 24076.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: rpiA, lpg0094 / Plasmid: LepnA.00944.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZZB7, ribose-5-phosphate isomerase
#2: Sugar ChemComp-R5P / RIBOSE-5-PHOSPHATE


Type: saccharide / Mass: 230.110 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Sugar ChemComp-5RP / RIBULOSE-5-PHOSPHATE


Type: saccharide / Mass: 230.110 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: LepnA.00944.a.B1.PS38423 at 22.85 mg/ml was mixed 1:1 with MCSG1(B8): 25.5% (w/v) PEG-4,000, 15% (v/v) Glycerol, 0.085 M Tris Base / Hydrochloric, 0.17 M Sodium Acetate, pH = 8.5.Crystals ...Details: LepnA.00944.a.B1.PS38423 at 22.85 mg/ml was mixed 1:1 with MCSG1(B8): 25.5% (w/v) PEG-4,000, 15% (v/v) Glycerol, 0.085 M Tris Base / Hydrochloric, 0.17 M Sodium Acetate, pH = 8.5.Crystals from tray 300294b8 were then soaked overnight mixed 1:1 with MCSG1(B8) condition suplemented with 5 mM ribulose-5-phosphate. Tray: 300294b8. Puck: kbr1-2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 23, 2018
RadiationMonochromator: Rigaku Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→45.247 Å / Num. obs: 29874 / % possible obs: 99.3 % / Redundancy: 4.066 % / Biso Wilson estimate: 32.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.074 / Χ2: 0.939 / Net I/σ(I): 15.57 / Num. measured all: 121457 / Scaling rejects: 94
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.052.5920.4492.2222020.7930.55199.6
2.05-2.112.9130.3942.921200.8090.47699.3
2.11-2.173.2170.3273.720940.8980.38899.5
2.17-2.243.4160.2844.5820070.9220.33498.7
2.24-2.313.5950.2395.8319180.9460.2898.7
2.31-2.393.9590.2146.4419350.9640.24799.4
2.39-2.484.4930.2127.2118390.9710.24199.5
2.48-2.584.6140.1738.8717670.980.19699.5
2.58-2.74.6450.13511.1717030.9880.15399.2
2.7-2.834.6550.10913.2116160.9920.12399.8
2.83-2.984.6970.08216.3315370.9950.09299.4
2.98-3.164.6510.06918.9614510.9970.07899.3
3.16-3.384.6920.05124.8913850.9980.05799.6
3.38-3.654.6850.03833.3612870.9990.04399.6
3.65-44.6130.03436.9511840.9990.03999.7
4-4.474.6110.02844.7610830.9990.03299.4
4.47-5.164.6450.02645.589560.9990.0399.3
5.16-6.324.6710.03636.068050.9990.0499.6
6.32-8.944.6030.02645.516290.9990.0398.7
8.94-45.2474.3030.02257.9235610.02597.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX(1.14_3228)refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EEP

6eep


Resolution: 2→45.247 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.75
RfactorNum. reflection% reflection
Rfree0.2028 2020 6.77 %
Rwork0.1542 --
obs0.1576 29816 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.85 Å2 / Biso mean: 31.424 Å2 / Biso min: 11.63 Å2
Refinement stepCycle: final / Resolution: 2→45.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3232 0 30 424 3686
Biso mean--34.23 39.66 -
Num. residues----435
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0001-2.05010.29081250.22671988211399
2.0501-2.10550.25441460.20861940208699
2.1055-2.16750.24621520.196319762128100
2.1675-2.23740.2861260.18721965209199
2.2374-2.31740.2341400.17451992213299
2.3174-2.41020.23891560.179219462102100
2.4102-2.51990.22581490.168419942143100
2.5199-2.65270.22021360.15819812117100
2.6527-2.81890.22161460.157219892135100
2.8189-3.03650.22811470.159219822129100
3.0365-3.3420.18521300.160520202150100
3.342-3.82530.1851430.132319992142100
3.8253-4.81870.16731780.115819732151100
4.8187-45.25890.16231460.14242051219799
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)
12.5942-0.39961.46370.86040.08031.8484-0.2944-0.52610.63230.28770.03750.0632-0.4388-0.18190.21740.32230.0065-0.05770.2381-0.09310.26053.455610.39125.368
22.4067-0.76191.01863.09592.1342.5961-0.0111-0.1420.7497-0.0582-0.14330.1296-0.6757-0.09320.25160.2664-0.0296-0.03350.165-0.10020.3393-10.620112.644614.884
33.9065-0.7222-1.44944.44051.59343.99920.1045-0.10790.6253-0.508-0.0425-0.2299-0.8450.0426-0.06120.2938-0.0516-0.03620.17030.00820.23110.349911.218713.4357
42.166-0.23790.63631.2004-0.17091.7083-0.0687-0.64670.26290.1076-0.10530.093-0.2134-0.09820.15380.2509-0.0502-0.00970.3024-0.06410.1702-2.24795.586625.4086
56.9482.38092.52226.48542.40913.75820.314-1.6046-0.00181.1865-0.4651-0.7626-0.08540.56640.10290.3715-0.0393-0.12530.5604-0.01650.280419.9771.221134.7846
67.5258-1.5378-0.16839.1504-2.27186.33990.0405-0.1006-0.4501-0.4081-0.11811.05440.3867-0.63930.11960.1814-0.0195-0.03290.3652-0.040.3061-36.0521-1.6801-0.192
74.11210.8035-1.32520.18660.06174.10380.12280.06470.4647-0.0429-0.28430.7446-0.6973-0.30750.05020.27630.1076-0.06710.2341-0.09130.3298-27.255511.55842.5191
83.9975-0.08930.03242.8872-1.03493.6254-0.01080.1310.0982-0.28-0.12090.1172-0.3205-0.26170.15260.22990.04-0.01490.1826-0.06120.167-24.11976.2255-3.6479
96.89950.95711.70571.3958-0.69841.1195-0.1357-0.32590.8303-0.0462-0.17630.2286-0.4374-0.11820.20820.30180.0776-0.00190.1685-0.01940.3081-18.551113.84252.4564
103.16720.26080.79211.5866-0.53811.17150.0713-0.3507-0.09860.1215-0.08440.230.053-0.4206-0.01210.1738-0.03220.04790.2532-0.03260.1531-23.9476-2.499911.9426
112.86690.46150.69013.0067-1.59743.36850.2619-0.1909-0.66120.0203-0.162-0.14860.2879-0.02250.00830.2378-0.0373-0.00410.15240.02610.2927-6.9278-12.439313.812
122.1541-0.26590.27522.036-0.2562.12240.1507-0.4868-0.2090.2617-0.15780.10650.0772-0.3060.00310.2132-0.08660.00510.25260.01430.1667-16.7008-5.491619.4865
133.95391.89842.79864.38250.8795.9173-0.1944-0.9440.27140.0846-0.27511.36190.0469-1.41520.4540.1841-0.00570.0280.5452-0.08210.4542-38.7982-1.09279.5153
144.5826-0.62332.53586.96141.42035.3011-0.0277-0.25-0.24820.23510.2958-0.35090.10680.3471-0.21580.132-0.01180.03470.24960.0390.141621.4415-4.478924.0532
155.0756-0.58260.86673.35292.35444.531-0.0824-0.1179-0.43730.29020.2451-0.23430.330.2819-0.14630.1942-0.01350.00570.17090.03690.207421.5815-7.706317.8933
166.4934-2.6161-0.92612.95841.53542.99170.12470.3469-0.2264-0.1229-0.13690.0715-0.0590.09950.06020.2039-0.071-0.00360.16720.02190.182915.7256-4.696510.1396
171.0081-0.89550.81731.1221-0.08261.82730.1137-0.5564-0.89130.0181-0.06190.07180.746-0.27140.04080.3511-0.0729-0.02150.25220.11270.3049.9402-15.018315.8456
182.0509-0.93991.13483.68760.48432.368-0.2144-0.69770.20760.42290.1139-0.2174-0.2237-0.16710.10870.1998-0.0302-0.01840.3307-0.03120.15719.18982.503927.3013
192.9707-0.4071.27851.31590.10781.32790.0724-0.5630.06620.2284-0.0926-0.0722-0.0370.0416-0.03320.1881-0.06710.00060.2539-0.00150.124610.2027-1.4724.9209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 120 through 134 )B120 - 134
2X-RAY DIFFRACTION2chain 'B' and (resid 135 through 147 )B135 - 147
3X-RAY DIFFRACTION3chain 'B' and (resid 148 through 164 )B148 - 164
4X-RAY DIFFRACTION4chain 'B' and (resid 165 through 202 )B165 - 202
5X-RAY DIFFRACTION5chain 'B' and (resid 203 through 216 )B203 - 216
6X-RAY DIFFRACTION6chain 'A' and (resid -1 through 15 )A-1 - 15
7X-RAY DIFFRACTION7chain 'A' and (resid 16 through 27 )A16 - 27
8X-RAY DIFFRACTION8chain 'A' and (resid 28 through 60 )A28 - 60
9X-RAY DIFFRACTION9chain 'A' and (resid 61 through 75 )A61 - 75
10X-RAY DIFFRACTION10chain 'A' and (resid 76 through 134 )A76 - 134
11X-RAY DIFFRACTION11chain 'A' and (resid 135 through 164 )A135 - 164
12X-RAY DIFFRACTION12chain 'A' and (resid 165 through 202 )A165 - 202
13X-RAY DIFFRACTION13chain 'A' and (resid 203 through 216 )A203 - 216
14X-RAY DIFFRACTION14chain 'B' and (resid 0 through 27 )B0 - 27
15X-RAY DIFFRACTION15chain 'B' and (resid 28 through 49 )B28 - 49
16X-RAY DIFFRACTION16chain 'B' and (resid 50 through 61 )B50 - 61
17X-RAY DIFFRACTION17chain 'B' and (resid 62 through 75 )B62 - 75
18X-RAY DIFFRACTION18chain 'B' and (resid 76 through 97 )B76 - 97
19X-RAY DIFFRACTION19chain 'B' and (resid 98 through 119 )B98 - 119

+
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://pdbjlvh1.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