[English] 日本語
Yorodumi
- PDB-5vjf: Class II fructose-1,6-bisphosphate aldolase of Helicobacter pylor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vjf
TitleClass II fructose-1,6-bisphosphate aldolase 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: 1.85 Å
AuthorsCoincon, M. / Sygusch, J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
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
DepositionApr 19, 2017Deposition 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 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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.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)68,29111
Polymers67,6022
Non-polymers6899
Water15,133840
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-130 kcal/mol
Surface area22470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.518, 88.046, 90.811
Angle α, β, γ (deg.)90.00, 100.39, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 33800.812 Da / Num. of mol.: 2 / Mutation: T48A, T67I
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

-
Non-polymers , 6 types, 849 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE / Dihydroxyacetone phosphate


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


Mass: 18.015 Da / Num. of mol.: 840 / 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: 2.3 Å3/Da / Density % sol: 46.49 %
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: NSLS / Beamline: X8C / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.85→39.488 Å / Num. obs: 50194 / % possible obs: 91.9 % / Redundancy: 2.6 % / Biso Wilson estimate: 15.1 Å2 / Rsym value: 0.06 / Net I/σ(I): 16.5

-
Processing

Software
NameVersionClassification
PHENIXdev_1134refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C4U
Resolution: 1.85→39.488 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.39
RfactorNum. reflection% reflection
Rfree0.1743 5111 10.18 %
Rwork0.1366 --
obs0.1404 50194 91.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→39.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4552 0 32 840 5424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064655
X-RAY DIFFRACTIONf_angle_d0.9246255
X-RAY DIFFRACTIONf_dihedral_angle_d12.5591750
X-RAY DIFFRACTIONf_chiral_restr0.055694
X-RAY DIFFRACTIONf_plane_restr0.004812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8710.26961350.18921276X-RAY DIFFRACTION82
1.871-1.89310.21011480.18451394X-RAY DIFFRACTION89
1.8931-1.91610.22851730.16561418X-RAY DIFFRACTION91
1.9161-1.94040.19791550.15491417X-RAY DIFFRACTION92
1.9404-1.96590.20231850.15271463X-RAY DIFFRACTION93
1.9659-1.99290.21441690.15571439X-RAY DIFFRACTION94
1.9929-2.02130.19171680.15161418X-RAY DIFFRACTION93
2.0213-2.05150.2091570.14691504X-RAY DIFFRACTION94
2.0515-2.08360.19651510.14291496X-RAY DIFFRACTION95
2.0836-2.11770.17561470.14011487X-RAY DIFFRACTION95
2.1177-2.15420.18012010.14021481X-RAY DIFFRACTION96
2.1542-2.19340.16111900.12761532X-RAY DIFFRACTION98
2.1934-2.23560.18331500.1281498X-RAY DIFFRACTION98
2.2356-2.28120.1681910.13581519X-RAY DIFFRACTION98
2.2812-2.33080.17361870.13231560X-RAY DIFFRACTION99
2.3308-2.3850.20091780.13211525X-RAY DIFFRACTION99
2.385-2.44460.20481870.1281515X-RAY DIFFRACTION99
2.4446-2.51070.17841670.13251582X-RAY DIFFRACTION99
2.5107-2.58460.18941860.1351538X-RAY DIFFRACTION100
2.5846-2.6680.18051900.13171548X-RAY DIFFRACTION99
2.668-2.76330.17191800.13231541X-RAY DIFFRACTION100
2.7633-2.8740.17351850.1321553X-RAY DIFFRACTION99
2.874-3.00470.16011660.12871569X-RAY DIFFRACTION99
3.0047-3.16310.17571660.13851529X-RAY DIFFRACTION99
3.1631-3.36110.17641530.12881583X-RAY DIFFRACTION99
3.3611-3.62050.15231570.11981562X-RAY DIFFRACTION98
3.6205-3.98450.13131990.12521528X-RAY DIFFRACTION99
3.9845-4.56040.14371700.1161529X-RAY DIFFRACTION98
4.5604-5.74270.14061590.13081557X-RAY DIFFRACTION97
5.7427-39.49650.20541610.18311522X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.1086-0.03540.12630.18120.0470.19370.00040.0323-0.1759-0.020.00870.06260.0572-0.14240.00370.0207-0.01640.00860.0713-0.03610.1005-7.9944-13.13672.4407
20.1593-0.01680.02550.15580.0810.3124-0.0206-0.01820.00280.0360.00310.0355-0.0362-0.0629-0.2461-0.0546-0.0189-0.0427-0.0513-0.0465-0.0318-2.8395-2.372313.811
30.032-0.0090.01130.24360.10950.2198-0.0114-0.0086-0.01970.0533-0.00610.03370.048-0.0435-0.095-0.0626-0.0831-0.0237-0.0622-0.03930.0134-0.0171-8.977515.1756
40.1759-0.0589-0.1190.0791-0.04620.2040.03050.016-0.08290.02640.013-0.07750.01510.0803-0.0223-0.0247-0.0419-0.03050.0143-0.06080.049613.4495-13.22277.9503
50.609-0.03170.40950.44950.03370.6687-0.05330.09720.0768-0.05550.0337-0.0906-0.07980.1317-0.14690.0134-0.0229-0.00380.03390.00330.04319.5634-6.01430.6228
60.8814-0.34540.14150.6148-0.03360.37670.05070.11730.0699-0.08390.0125-0.2306-0.01830.12840.18080.00710.00180.05820.0247-0.07660.044512.1872-13.3137-4.6144
70.9927-0.56980.15820.370.12451.10670.02050.03530.179-0.0820.0142-0.0506-0.154-0.0271-0.29510.0079-0.0040.04310.0159-0.05530.04816.2949-3.0691-3.4083
80.04950.01020.05140.0242-0.020.15480.01270.0915-0.0081-0.1196-0.0268-0.0475-0.03230.0567-0.08340.1368-0.01590.04440.1396-0.05010.08145.3695-6.0167-14.3652
90.0969-0.0373-0.13420.18530.12180.21490.04270.01270.0437-0.07320.0149-0.0244-0.10480.02070.06170.05580.0091-0.0077-0.0326-0.01620.03591.6613-5.636-5.9101
100.06360.02230.01350.0128-0.01810.09790.07990.03170.1451-0.0580.0104-0.0006-0.0737-0.01130.10290.42160.03960.05020.0929-0.00680.2268-0.376913.4187-3.6542
110.06220.004-0.03290.0062-0.01430.04350.05820.07580.0363-0.1021-0.01380.0104-0.1563-0.03770.05370.16740.05310.00290.1421-0.00670.0002-4.874-1.1926-14.3444
120.0673-0.04910.05740.1105-0.10650.1672-0.03390.00540.01860.04020.00510.0128-0.0735-0.02280.01470.0350.0192-0.01210.0042-0.02550.0229-3.41911.4573-1.1829
130.0077-0.03650.00920.1716-0.0410.0095-0.02420.02490.0566-0.04030.01710.0711-0.0615-0.0319-0.06370.15840.0842-0.01190.02770.03420.0566-7.274919.106312.8674
140.0186-0.00260.0170.0001-0.00130.0144-0.00120.07190.0926-0.023-0.0247-0.088-0.16450.04470.00040.27320.00920.00620.0967-0.00140.1486-1.845819.16596.926
150.0598-0.02320.00590.0389-0.03280.032-0.00690.03080.027-0.05250.00980.0605-0.0664-0.07290.04450.12780.081-0.02450.18720.02110.0788-11.67425.9056-4.1393
160.1288-0.03350.07890.1061-0.13590.1915-0.02140.00660.07320.04090.00820.0458-0.0968-0.02030.07-0.00140.0882-0.0137-0.15690.01080.0136-2.95499.805813.9201
170.1192-0.0658-0.0020.1635-0.01040.1108-0.00950.0225-0.00450.02930.00730.0256-0.0432-0.09070.0290.02630.0422-0.02890.0303-0.01310.0509-8.67146.12419.2083
180.13960.07940.03740.04590.02140.05830.0685-0.0294-0.08240.0041-0.0409-0.04550.14850.0724-0.04310.04970.0389-0.00720.10330.07690.082112.971-12.965847.1264
190.2054-0.01830.14940.1702-0.01730.4284-0.03430.0149-0.0143-0.0536-0.0129-0.0415-0.02020.11710.1564-0.01510.00280.00640.02680.0195-0.02411.0171-2.387236.2078
200.02190.0236-0.01720.07170.01140.0572-0.0068-0.01340.02160.00410.0110.0355-0.0144-0.0517-0.0101-0.00180.0125-0.03740.02210.05130.0054-5.8024-1.776733.4216
210.36050.12840.02530.2039-0.08770.2943-0.02880.0437-0.0094-0.045-0.0011-0.04730.02710.0609-0.0478-0.05640.00820.0156-0.02790.02960.0037.1685-9.984332.2646
220.0184-0.0093-0.00670.0075-0.00560.0280.0244-0.0523-0.0596-0.0345-0.01480.1029-0.0106-0.0755-00.0465-0.0053-0.01380.09890.02690.0996-7.6196-9.886842.8958
230.53950.22340.52310.43340.15260.5191-0.0206-0.12190.03910.0565-0.00280.1073-0.0261-0.127-0.2224-0.02590.02950.00480.04040.01710.0395-4.5039-5.87548.9469
240.33290.14590.09630.72410.28510.28490.0559-0.14090.04140.134-0.06340.17170.0199-0.1037-0.0181-0.0104-0.04640.06570.09260.09570.0644-7.0494-13.138154.2393
251.46150.16090.15450.1-0.02861.05490.0091-0.15560.30310.0754-0.01560.0824-0.1348-0.0365-0.18270.02320.01420.03290.09310.01950.1196-1.4002-2.897552.882
260.62520.3786-0.10020.9823-0.10110.08420.0588-0.30560.030.30830.050.1206-0.0533-0.16170.0450.08220.03550.00010.23580.07080.06251.1564-5.667560.7024
270.0021-0.00510.00540.0071-0.00930.010.06-0.12330.17910.041-0.0153-0.0094-0.10480.049400.41280.048-0.03220.2824-0.0310.20825.395213.802552.8622
280.4378-0.11420.15460.4325-0.31190.3989-0.0131-0.29810.02510.2677-0.0774-0.0472-0.26560.0796-0.03240.1169-0.0112-0.02920.16810.0134-0.00699.20370.392357.5297
290.2014-0.04520.07570.1335-0.16490.2059-0.0134-0.10330.12420.1172-0.02720.0446-0.137-0.00310.06470.1876-0.0457-0.07230.0493-0.07690.12029.514119.352739.4425
300.04030.0311-0.00860.10180.02480.0147-0.0195-0.04390.05030.0645-0.0155-0.0673-0.05690.05580.05330.0901-0.0416-0.04930.219-0.01570.104316.67576.222553.6355
310.13740.1313-0.00250.2070.11340.1542-0.0226-0.06450.0362-0.08910.0052-0.0463-0.10890.08780.01590.0204-0.0486-0.0295-0.05540.0170.058211.3377.715332.3682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 57 )
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 86 )
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 96 )
5X-RAY DIFFRACTION5chain 'A' and (resid 97 through 109 )
6X-RAY DIFFRACTION6chain 'A' and (resid 110 through 127 )
7X-RAY DIFFRACTION7chain 'A' and (resid 128 through 139 )
8X-RAY DIFFRACTION8chain 'A' and (resid 153 through 167 )
9X-RAY DIFFRACTION9chain 'A' and (resid 168 through 177 )
10X-RAY DIFFRACTION10chain 'A' and (resid 178 through 192 )
11X-RAY DIFFRACTION11chain 'A' and (resid 193 through 203 )
12X-RAY DIFFRACTION12chain 'A' and (resid 204 through 216 )
13X-RAY DIFFRACTION13chain 'A' and (resid 217 through 225 )
14X-RAY DIFFRACTION14chain 'A' and (resid 226 through 237 )
15X-RAY DIFFRACTION15chain 'A' and (resid 238 through 247 )
16X-RAY DIFFRACTION16chain 'A' and (resid 248 through 272 )
17X-RAY DIFFRACTION17chain 'A' and (resid 273 through 307 )
18X-RAY DIFFRACTION18chain 'B' and (resid 1 through 15 )
19X-RAY DIFFRACTION19chain 'B' and (resid 16 through 49 )
20X-RAY DIFFRACTION20chain 'B' and (resid 50 through 57 )
21X-RAY DIFFRACTION21chain 'B' and (resid 58 through 81 )
22X-RAY DIFFRACTION22chain 'B' and (resid 82 through 96 )
23X-RAY DIFFRACTION23chain 'B' and (resid 97 through 109 )
24X-RAY DIFFRACTION24chain 'B' and (resid 110 through 127 )
25X-RAY DIFFRACTION25chain 'B' and (resid 128 through 139 )
26X-RAY DIFFRACTION26chain 'B' and (resid 153 through 177 )
27X-RAY DIFFRACTION27chain 'B' and (resid 178 through 192 )
28X-RAY DIFFRACTION28chain 'B' and (resid 193 through 216 )
29X-RAY DIFFRACTION29chain 'B' and (resid 217 through 237 )
30X-RAY DIFFRACTION30chain 'B' and (resid 238 through 247 )
31X-RAY DIFFRACTION31chain 'B' and (resid 248 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