[English] 日本語
Yorodumi
- PDB-4f2d: Crystal Structure of Escherichia coli L-arabinose Isomerase (ECAI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f2d
TitleCrystal Structure of Escherichia coli L-arabinose Isomerase (ECAI) complexed with Ribitol
ComponentsL-arabinose isomerase
KeywordsISOMERASE / Structural Genomics / PSI-1 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / Sugar Binding
Function / homology
Function and homology information


L-arabinose isomerase / L-arabinose isomerase activity / L-arabinose catabolic process to xylulose 5-phosphate / arabinose catabolic process / manganese ion binding / cytosol
Similarity search - Function
Rossmann fold - #10940 / L-arabinose isomerase / L-arabinose isomerase, C-terminal / L-arabinose isomerase, N-terminal domain superfamily / L-arabinose isomerase / 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
ACETIC ACID / : / D-ribitol / L-arabinose isomerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsManjasetty, B.A. / Burley, S.K. / Almo, S.C. / Chance, M.R. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Escherichia coli L-arabinose Isomerase (ECAI) complexed with Ribitol
Authors: Manjasetty, B.A. / Burley, S.K. / Almo, S.C. / Chance, M.R.
History
DepositionMay 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-arabinose isomerase
B: L-arabinose isomerase
C: L-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,58210
Polymers170,9013
Non-polymers6817
Water3,981221
1
A: L-arabinose isomerase
B: L-arabinose isomerase
C: L-arabinose isomerase
hetero molecules

A: L-arabinose isomerase
B: L-arabinose isomerase
C: L-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,16520
Polymers341,8026
Non-polymers1,36314
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area42190 Å2
ΔGint-235 kcal/mol
Surface area94910 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15190 Å2
ΔGint-113 kcal/mol
Surface area53360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.472, 116.472, 214.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-780-

HOH

DetailsThe biological assembly is a hexamer generated from the trimer in the asymmetric unit

-
Components

#1: Protein L-arabinose isomerase /


Mass: 56966.992 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: araA, b0062, JW0061, UTI89_C0067 / Plasmid: PET T7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08202, L-arabinose isomerase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-RB0 / D-ribitol / Ribitol


Mass: 152.146 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C5H12O5
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, TRISODIUM CITRATE DIHYDRATE, Ribitol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.1
SYNCHROTRONNSLS X3A20.979
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDJul 18, 2006MIRRORS
MAR CCD 165 mm2CCDMIRRORS
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI111SINGLE WAVELENGTHMx-ray1
2SI111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.9791
ReflectionResolution: 2.3→20 Å / Num. obs: 85584 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 52 Å2 / Rsym value: 0.073 / Net I/σ(I): 22.3

-
Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
REFMAC5.6.0116refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AJT

2ajt


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 21.053 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25505 3746 5 %RANDOM
Rwork0.21184 ---
obs0.21401 70507 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.847 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20.68 Å20 Å2
2--1.37 Å20 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11522 0 37 221 11780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0211847
X-RAY DIFFRACTIONr_bond_other_d0.0030.027718
X-RAY DIFFRACTIONr_angle_refined_deg1.0771.94516096
X-RAY DIFFRACTIONr_angle_other_deg1.218318794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.18751491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34924.378555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9151714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2331559
X-RAY DIFFRACTIONr_chiral_restr0.0620.21773
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113420
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022459
X-RAY DIFFRACTIONr_rigid_bond_restr8.025319565
X-RAY DIFFRACTIONr_sphericity_free42.407559
X-RAY DIFFRACTIONr_sphericity_bonded7.585519457
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 225 -
Rwork0.308 4068 -
obs--83.9 %
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)
10.6913-0.0254-0.01010.223-0.25671.4406-0.05790.09520.008-0.1740.01130.0646-0.0120.25440.04660.4644-0.1032-0.03780.08310.03710.247961.8034.5322.95
20.2411-0.07990.22960.4397-0.31961.6565-0.01190.0239-0.1157-0.04090.09710.17920.4535-0.2244-0.08520.4903-0.0952-0.01590.05960.03820.370739.116-23.32534.661
30.26470.24120.13081.0041-0.53961.54050.03780.134-0.1707-0.2447-0.2547-0.13010.51151.00440.21680.53090.40160.08450.68530.12160.227985.849-23.30934.341
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 174
2X-RAY DIFFRACTION1A175 - 354
3X-RAY DIFFRACTION1A355 - 498
4X-RAY DIFFRACTION2B1 - 174
5X-RAY DIFFRACTION2B175 - 354
6X-RAY DIFFRACTION2B355 - 498
7X-RAY DIFFRACTION3C1 - 174
8X-RAY DIFFRACTION3C175 - 354
9X-RAY DIFFRACTION3C355 - 498

+
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