[English] 日本語
Yorodumi
- PDB-7ch3: Crystal structure of Arabinose isomerase from hyper thermophilic ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ch3
TitleCrystal structure of Arabinose isomerase from hyper thermophilic bacterium Thermotoga maritima (TMAI) triple mutant (K264A, E265A, K266A)
ComponentsL-arabinose isomerase
KeywordsISOMERASE / Arabinose isomerase from hyperthermophile
Function / homology
Function and homology information


L-arabinose isomerase / L-arabinose isomerase activity / L-arabinose catabolic process to D-xylulose 5-phosphate / manganese ion binding / cytosol
Similarity search - Function
Rossmann fold - #10940 / : / : / L-arabinose isomerase central domain / L-arabinose isomerase / L-arabinose isomerase, C-terminal / L-arabinose isomerase, N-terminal domain superfamily / L-arabinose isomerase N-terminal domain / L-arabinose isomerase C-terminal domain / L-fucose/L-arabinose isomerase, C-terminal ...Rossmann fold - #10940 / : / : / L-arabinose isomerase central domain / L-arabinose isomerase / L-arabinose isomerase, C-terminal / L-arabinose isomerase, N-terminal domain superfamily / L-arabinose isomerase N-terminal domain / L-arabinose isomerase C-terminal domain / L-fucose/L-arabinose isomerase, C-terminal / L-fucose isomerase, N-terminal/central domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / L-arabinose isomerase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.61 Å
AuthorsCao, T.P. / Dhanasingh, I. / Sung, J.Y. / Shin, S.M. / Lee, D.W. / Lee, S.H.
CitationJournal: To Be Published
Title: Crystal structure of Arabinose isomerase from hyper thermophilic bacterium Thermotoga maritima (TMAI) triple mutant (K264A, E265A, K266A)
Authors: Cao, T.P. / Dhanasingh, I. / Sung, J.Y. / Shin, S.M. / Lee, D.W. / Lee, S.H.
History
DepositionJul 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-arabinose isomerase
B: L-arabinose isomerase
C: L-arabinose isomerase
D: L-arabinose isomerase
E: L-arabinose isomerase
F: L-arabinose isomerase
G: L-arabinose isomerase
H: L-arabinose isomerase
I: L-arabinose isomerase
J: L-arabinose isomerase
K: L-arabinose isomerase
L: L-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)679,73330
Polymers678,74412
Non-polymers98918
Water34219
1
A: L-arabinose isomerase
B: L-arabinose isomerase
C: L-arabinose isomerase
D: L-arabinose isomerase
F: L-arabinose isomerase
H: L-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)339,86615
Polymers339,3726
Non-polymers4949
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43730 Å2
ΔGint-254 kcal/mol
Surface area92760 Å2
MethodPISA
2
E: L-arabinose isomerase
G: L-arabinose isomerase
I: L-arabinose isomerase
J: L-arabinose isomerase
K: L-arabinose isomerase
L: L-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)339,86615
Polymers339,3726
Non-polymers4949
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43910 Å2
ΔGint-246 kcal/mol
Surface area94020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.424, 113.913, 160.833
Angle α, β, γ (deg.)81.080, 81.150, 88.890
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 1 through 218 or resid 245 through 495))
31(chain C and (resid 1 through 218 or resid 245 through 495))
41(chain D and (resid 1 through 218 or resid 245 through 495))
51(chain E and (resid 1 through 218 or resid 245 through 495))
61(chain F and (resid 1 through 218 or resid 245 through 495))
71(chain G and (resid 1 through 218 or resid 245 through 495))
81(chain H and (resid 1 through 218 or resid 245 through 495))
91(chain I and (resid 1 through 218 or resid 245 through 495))
101(chain J and (resid 1 through 218 or resid 245 through 495))
111(chain K and (resid 1 through 218 or resid 245 through 495))
121(chain L and (resid 1 through 218 or resid 245 through 495))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLYSLYSchain AAA1 - 4951 - 495
21METMETVALVAL(chain B and (resid 1 through 218 or resid 245 through 495))BB1 - 2181 - 218
22SERSERLYSLYS(chain B and (resid 1 through 218 or resid 245 through 495))BB245 - 495245 - 495
31METMETVALVAL(chain C and (resid 1 through 218 or resid 245 through 495))CC1 - 2181 - 218
32SERSERLYSLYS(chain C and (resid 1 through 218 or resid 245 through 495))CC245 - 495245 - 495
41METMETVALVAL(chain D and (resid 1 through 218 or resid 245 through 495))DD1 - 2181 - 218
42SERSERLYSLYS(chain D and (resid 1 through 218 or resid 245 through 495))DD245 - 495245 - 495
51METMETVALVAL(chain E and (resid 1 through 218 or resid 245 through 495))EE1 - 2181 - 218
52SERSERLYSLYS(chain E and (resid 1 through 218 or resid 245 through 495))EE245 - 495245 - 495
61METMETVALVAL(chain F and (resid 1 through 218 or resid 245 through 495))FF1 - 2181 - 218
62SERSERLYSLYS(chain F and (resid 1 through 218 or resid 245 through 495))FF245 - 495245 - 495
71METMETVALVAL(chain G and (resid 1 through 218 or resid 245 through 495))GG1 - 2181 - 218
72SERSERLYSLYS(chain G and (resid 1 through 218 or resid 245 through 495))GG245 - 495245 - 495
81METMETVALVAL(chain H and (resid 1 through 218 or resid 245 through 495))HH1 - 2181 - 218
82SERSERLYSLYS(chain H and (resid 1 through 218 or resid 245 through 495))HH245 - 495245 - 495
91METMETVALVAL(chain I and (resid 1 through 218 or resid 245 through 495))II1 - 2181 - 218
92SERSERLYSLYS(chain I and (resid 1 through 218 or resid 245 through 495))II245 - 495245 - 495
101METMETVALVAL(chain J and (resid 1 through 218 or resid 245 through 495))JJ1 - 2181 - 218
102SERSERLYSLYS(chain J and (resid 1 through 218 or resid 245 through 495))JJ245 - 495245 - 495
111METMETVALVAL(chain K and (resid 1 through 218 or resid 245 through 495))KK1 - 2181 - 218
112SERSERLYSLYS(chain K and (resid 1 through 218 or resid 245 through 495))KK245 - 495245 - 495
121METMETVALVAL(chain L and (resid 1 through 218 or resid 245 through 495))LL1 - 2181 - 218
122SERSERLYSLYS(chain L and (resid 1 through 218 or resid 245 through 495))LL245 - 495245 - 495

-
Components

#1: Protein
L-arabinose isomerase


Mass: 56561.984 Da / Num. of mol.: 12 / Mutation: K264A, E265A, K266A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Gene: araA, TM_0276 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9WYB3, L-arabinose isomerase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / Details: 100mM Tris pH 8.5, 2% Tacismate pH 8, 15% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 68198 / % possible obs: 98.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.053 / Rrim(I) all: 0.102 / Χ2: 0.707 / Net I/σ(I): 9 / Num. measured all: 252359
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.6-3.663.60.48633690.6320.2970.571197.3
3.66-3.733.70.41133740.6860.2540.4851.01597.8
3.73-3.83.60.34734280.8540.2110.4070.79497.9
3.8-3.883.70.36733590.8880.2230.4310.81998.1
3.88-3.963.70.27434520.920.1660.3210.76798.2
3.96-4.053.70.22633650.9320.1380.2650.76498.6
4.05-4.163.70.19933940.9470.1210.2330.7998.5
4.16-4.273.70.16834000.9290.1020.1980.84999
4.27-4.393.70.13834940.890.0850.1631.03999.2
4.39-4.543.80.09934250.970.060.1160.73399.3
4.54-4.73.80.07534020.980.0450.0870.76899.2
4.7-4.893.80.06234690.9790.0360.0720.62999.4
4.89-5.113.80.05834300.9810.0340.0670.58499.5
5.11-5.383.80.05634330.980.0330.0650.5799.5
5.38-5.713.80.05734480.9730.0340.0670.56899.6
5.71-6.153.80.04834500.9760.0280.0560.50299.6
6.15-6.773.80.03834580.9830.0220.0440.48199.7
6.77-7.753.70.02634260.9890.0160.0310.45799.7
7.75-9.753.60.02134430.9880.0120.0240.49199.1
9.75-503.20.02231790.9890.0140.0260.54392.1

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HXG

2hxg


Resolution: 3.61→33.11 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2799 3336 4.98 %
Rwork0.2316 63677 -
obs0.2341 67013 96.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204.2 Å2 / Biso mean: 73.6774 Å2 / Biso min: 15.86 Å2
Refinement stepCycle: final / Resolution: 3.61→33.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47398 0 18 19 47435
Biso mean--90.91 35.7 -
Num. residues----5914
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A17076X-RAY DIFFRACTION7.063TORSIONAL
12B17076X-RAY DIFFRACTION7.063TORSIONAL
13C17076X-RAY DIFFRACTION7.063TORSIONAL
14D17076X-RAY DIFFRACTION7.063TORSIONAL
15E17076X-RAY DIFFRACTION7.063TORSIONAL
16F17076X-RAY DIFFRACTION7.063TORSIONAL
17G17076X-RAY DIFFRACTION7.063TORSIONAL
18H17076X-RAY DIFFRACTION7.063TORSIONAL
19I17076X-RAY DIFFRACTION7.063TORSIONAL
110J17076X-RAY DIFFRACTION7.063TORSIONAL
111K17076X-RAY DIFFRACTION7.063TORSIONAL
112L17076X-RAY DIFFRACTION7.063TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.61-3.660.3004980.28671835193365
3.66-3.710.34251280.29062336246485
3.71-3.770.33881180.27762488260690
3.77-3.830.30291510.28162627277895
3.83-3.90.31951420.27732633277596
3.9-3.970.29891430.27692740288397
3.97-4.050.30051270.26012671279898
4.05-4.130.32521280.26342714284298
4.13-4.220.31351440.27032725286998
4.22-4.320.33981470.27242710285799
4.32-4.420.29171460.24992709285598
4.42-4.540.26831310.22622767289899
4.54-4.680.27451560.21282712286899
4.68-4.830.28341480.2132743289199
4.83-50.26781330.21422742287599
5-5.20.23791560.207327602916100
5.2-5.430.32291280.22222760288899
5.43-5.720.26231400.230127402880100
5.72-6.070.27481560.226527262882100
6.07-6.540.30591380.240127462884100
6.54-7.190.25951690.215627492918100
7.19-8.220.20571380.177927402878100
8.22-10.30.21291550.16592724287999
10.3-33.110.28361160.2122580269693
Refinement TLS params.Method: refined / Origin x: -18.4847 Å / Origin y: -4.1574 Å / Origin z: -16.3098 Å
111213212223313233
T0.1153 Å20.0087 Å20.1375 Å2-0.1342 Å2-0.0956 Å2--0.2946 Å2
L0.5814 °2-0.1722 °20.4299 °2-0.3642 °2-0.2957 °2--1.007 °2
S-0.0247 Å °0.0513 Å °0.043 Å °-0.0501 Å °-0.0062 Å °-0.0464 Å °0.1275 Å °-0.086 Å °0.0153 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 495
2X-RAY DIFFRACTION1allB1 - 495
3X-RAY DIFFRACTION1allC1 - 495
4X-RAY DIFFRACTION1allD1 - 495
5X-RAY DIFFRACTION1allE1 - 495
6X-RAY DIFFRACTION1allF1 - 495
7X-RAY DIFFRACTION1allG1 - 495
8X-RAY DIFFRACTION1allH1 - 495
9X-RAY DIFFRACTION1allI1 - 495
10X-RAY DIFFRACTION1allJ1 - 495
11X-RAY DIFFRACTION1allK1 - 495
12X-RAY DIFFRACTION1allL1 - 495
13X-RAY DIFFRACTION1allM1 - 18
14X-RAY DIFFRACTION1allN1 - 19

+
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