[English] 日本語
Yorodumi
- PDB-5ucn: Class II fructose-1,6-bisphosphate aldolase E142A variant of Heli... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ucn
TitleClass II fructose-1,6-bisphosphate aldolase E142A variant of Helicobacter pylori with DHAP
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / Glycolysis / Metalloenzyme
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / glycolytic process / zinc ion binding
Similarity search - Function
Fructose-1,6-bisphosphate aldolase, class 2 / : / Fructose-bisphosphate aldolase class-II signature 1. / Fructose-bisphosphate aldolase class-II signature 2. / Fructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase class-II / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1,3-DIHYDROXYACETONEPHOSPHATE / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsJacques, B. / Sygusch, J.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases.
Authors: Jacques, B. / Coincon, M. / Sygusch, J.
History
DepositionDec 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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: Fructose-bisphosphate aldolase
B: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,13310
Polymers67,4862
Non-polymers6488
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-212 kcal/mol
Surface area21880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.308, 62.612, 64.507
Angle α, β, γ (deg.)82.17, 75.88, 74.17
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Fructose-bisphosphate aldolase / FBPA / Fructose-1 / 6-bisphosphate aldolase


Mass: 33742.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: fba, HP_0176 / Production host: Escherichia coli (E. coli) / References: UniProt: P56109, fructose-bisphosphate aldolase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE


Mass: 170.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.19 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, PEG 1000, Calcium acetate, Tris-Acetic acid buffer

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.67→45 Å / Num. obs: 58107 / % possible obs: 86.8 % / Redundancy: 2.4 % / Biso Wilson estimate: 14 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.099 / Net I/σ(I): 6.9
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 0.69 / % possible all: 39.1

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C4U

3c4u


Resolution: 1.67→44.98 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 25.43
RfactorNum. reflection% reflection
Rfree0.2081 2678 5.13 %
Rwork0.1714 --
obs0.1733 52189 77.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.67→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4520 0 26 351 4897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064698
X-RAY DIFFRACTIONf_angle_d0.7926326
X-RAY DIFFRACTIONf_dihedral_angle_d13.42844
X-RAY DIFFRACTIONf_chiral_restr0.046694
X-RAY DIFFRACTIONf_plane_restr0.005822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.666-1.69630.4793340.3435727X-RAY DIFFRACTION22
1.6963-1.72890.4103630.34941196X-RAY DIFFRACTION36
1.7289-1.76420.3169760.32061497X-RAY DIFFRACTION45
1.7642-1.80260.3641120.29781792X-RAY DIFFRACTION54
1.8026-1.84450.32731180.27922124X-RAY DIFFRACTION64
1.8445-1.89060.28041190.26552335X-RAY DIFFRACTION70
1.8906-1.94170.32041370.24362545X-RAY DIFFRACTION76
1.9417-1.99890.23691330.23032744X-RAY DIFFRACTION82
1.9989-2.06340.24971610.2132908X-RAY DIFFRACTION87
2.0634-2.13710.23121700.19192924X-RAY DIFFRACTION88
2.1371-2.22270.24241570.16813047X-RAY DIFFRACTION91
2.2227-2.32390.23091610.1633065X-RAY DIFFRACTION92
2.3239-2.44640.18681780.16363116X-RAY DIFFRACTION94
2.4464-2.59960.19081670.16423182X-RAY DIFFRACTION95
2.5996-2.80030.18081720.16773212X-RAY DIFFRACTION96
2.8003-3.08210.24711820.183219X-RAY DIFFRACTION97
3.0821-3.52790.20091800.15533275X-RAY DIFFRACTION98
3.5279-4.44420.15411720.12173296X-RAY DIFFRACTION99
4.4442-44.9960.13761860.12613307X-RAY DIFFRACTION99
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)
10.05340.04460.00540.0584-0.01740.0567-0.0342-0.10640.0494-0.03350.00730.00090.01240.0035-0.01730.08140.01390.00280.1432-0.01050.1035-10.026119.3518-22.6616
20.00360.0009-0.00010.00290.0003-00.0005-0.04120.0351-0.0014-0.0004-0.0076-0.0231-0.0345-00.11650.0294-0.00190.1854-0.04710.1362-12.46333.8149-15.1287
30.0040.003-0.00060.0023-0.00090.00080.0095-0.02880.0225-0.02860.0360.0054-0.0217-0.0046-00.1626-0.00660.00770.1895-0.03870.1589-4.869138.8807-19.9739
40.0626-0.0171-0.03480.03110.00780.0197-0.0079-0.00350.0215-0.13570.0434-0.0092-0.02570.02920.04250.2131-0.0820.02560.10570.00410.0938-1.914128.2749-38.7774
50.0545-0.00270.04540.0398-0.02970.071-0.0160.0488-0.08480.0130.00950.0066-0.04240.0174-0.01420.07140.00490.00870.07480.00950.1198-11.6015-4.3253-45.3035
60.00340.0010.00290.00020.00090.00340.0220.0251-0.0511-0.0332-0.0117-0.017-0.00690.0035-00.12880.01790.02560.1123-0.02080.1668-9.2271-12.4706-59.4279
70.00090.00010.00120.000400.0013-0.02290.0498-0.007-0.0152-0.038-0.0028-0.00730.0102-00.1470.0213-0.00020.1388-0.02270.1512-16.7767-8.0468-64.7114
80.0662-0.02660.00410.01870.00040.0459-0.00490.02590.0033-0.0191-0.02840.0095-0.12430.0043-0.05460.19670.0216-0.05980.08380.02590.0912-19.879711.322-54.9075
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 127 )
2X-RAY DIFFRACTION2chain 'A' and (resid 128 through 184 )
3X-RAY DIFFRACTION3chain 'A' and (resid 185 through 216 )
4X-RAY DIFFRACTION4chain 'A' and (resid 217 through 307 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 127 )
6X-RAY DIFFRACTION6chain 'B' and (resid 128 through 184 )
7X-RAY DIFFRACTION7chain 'B' and (resid 185 through 216 )
8X-RAY DIFFRACTION8chain 'B' and (resid 217 through 307 )

+
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