[English] 日本語
Yorodumi
- PDB-5u7s: Crystal structure of a fructose-bisphosphate aldolase, class II, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5u7s
TitleCrystal structure of a fructose-bisphosphate aldolase, class II, Calvin cycle subtype from Acinetobacter baumannii
ComponentsFructose-1,6-bisphosphate aldolase
KeywordsLYASE / structural genomics / aldolase / National Institute of Allergy and Infectious Diseases / NIAID / ESKAPE pathogen / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process / zinc ion binding
Similarity search - Function
Fructose-bisphosphate aldolase, class II, Calvin cycle subtype / 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
CITRIC ACID / FORMIC ACID / Fructose-1,6-bisphosphate aldolase
Similarity search - Component
Biological speciesAcinetobacter baumannii (unknown)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a fructose-bisphosphate aldolase, class II, Calvin cycle subtype from Acinetobacter baumannii
Authors: Edwards, T.E. / Abendroth, J. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionDec 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fructose-1,6-bisphosphate aldolase
B: Fructose-1,6-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1185
Polymers76,8572
Non-polymers2613
Water1,31573
1
A: Fructose-1,6-bisphosphate aldolase
B: Fructose-1,6-bisphosphate aldolase
hetero molecules

A: Fructose-1,6-bisphosphate aldolase
B: Fructose-1,6-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,23710
Polymers153,7144
Non-polymers5226
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12240 Å2
ΔGint-84 kcal/mol
Surface area43700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.110, 83.120, 99.390
Angle α, β, γ (deg.)90.000, 131.980, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -2 through 0 or (resid 1...
21(chain B and ((resid -2 through -1 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid -2 through 0 or (resid 1...A-2 - 0
121(chain A and (resid -2 through 0 or (resid 1...A1 - 2
131(chain A and (resid -2 through 0 or (resid 1...A-2 - 345
141(chain A and (resid -2 through 0 or (resid 1...A-2 - 345
151(chain A and (resid -2 through 0 or (resid 1...A-2 - 345
161(chain A and (resid -2 through 0 or (resid 1...A-2 - 345
211(chain B and ((resid -2 through -1 and (name N...B-2 - -1
221(chain B and ((resid -2 through -1 and (name N...B-2 - 345
231(chain B and ((resid -2 through -1 and (name N...B-2 - 345
241(chain B and ((resid -2 through -1 and (name N...B-2 - 345
251(chain B and ((resid -2 through -1 and (name N...B-2 - 345

-
Components

#1: Protein Fructose-1,6-bisphosphate aldolase / Fructose-bisphosphate aldolase class 2 / Fructose-bisphosphate aldolase class II / Fructose- ...Fructose-bisphosphate aldolase class 2 / Fructose-bisphosphate aldolase class II / Fructose-bisphosphate aldolase / class II / Calvin cycle subtype


Mass: 38428.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (unknown) / Gene: fbaA / Production host: Escherichia coli (E. coli) / References: UniProt: V5VDS0, fructose-bisphosphate aldolase
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: AcbaC.01416.a.A1.PS02365 at 24 mg/mL against Morpheus G6 10% PEG 8000, 20% EG, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM trisodium potassium tartrate, 20 mM sodium oxamate, 0.1 M ...Details: AcbaC.01416.a.A1.PS02365 at 24 mg/mL against Morpheus G6 10% PEG 8000, 20% EG, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM trisodium potassium tartrate, 20 mM sodium oxamate, 0.1 M MOPS/Hepes pH 7.5, crystal ID 262645g6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→40.484 Å / Num. obs: 26739 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 6.669 % / Biso Wilson estimate: 46.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.079 / Χ2: 1.008 / Net I/σ(I): 16.15 / Num. measured all: 178325 / Scaling rejects: 7409
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.5-2.574.2740.4732.590.933181.4
2.57-2.644.7690.4682.90.949190.1
2.64-2.715.7490.3943.790.971195.6
2.71-2.86.9990.3335.130.983193.9
2.8-2.897.3810.2716.760.985193.7
2.89-2.997.3530.2268.190.986193.3
2.99-3.17.320.16610.30.993194.5
3.1-3.237.3180.15111.440.994194
3.23-3.377.280.11614.660.995195.1
3.37-3.547.1290.08619.260.997196.7
3.54-3.737.0220.07621.870.997197.5
3.73-3.956.9410.06724.240.997195.3
3.95-4.236.850.05726.770.998194.3
4.23-4.566.7730.05329.730.998196.6
4.56-56.8040.04531.820.998197.4
5-5.596.9850.04832.10.998198.2
5.59-6.467.1510.04632.370.999198.6
6.46-7.917.0430.04136.650.998198.3
7.91-11.186.9510.03241.750.999198.7
11.18-40.4846.8050.03641.980.997195.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40.484 Å / SU ML: 0.3 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 31.7
RfactorNum. reflection% reflection
Rfree0.2625 1352 5.06 %
Rwork0.1992 --
obs0.2024 26717 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 157.51 Å2 / Biso mean: 67.5301 Å2 / Biso min: 31.63 Å2
Refinement stepCycle: final / Resolution: 2.5→40.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4824 0 17 73 4914
Biso mean--62.9 53.64 -
Num. residues----653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084936
X-RAY DIFFRACTIONf_angle_d0.9726727
X-RAY DIFFRACTIONf_chiral_restr0.058777
X-RAY DIFFRACTIONf_plane_restr0.007891
X-RAY DIFFRACTIONf_dihedral_angle_d13.4762934
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2749X-RAY DIFFRACTION10.5TORSIONAL
12B2749X-RAY DIFFRACTION10.5TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.58940.3361980.27562242234084
2.5894-2.69310.34381540.26022466262094
2.6931-2.81560.29631490.2712506265594
2.8156-2.9640.36361340.25832500263494
2.964-3.14970.33441320.24752541267394
3.1497-3.39280.33091390.24412542268195
3.3928-3.7340.25721640.20072584274898
3.734-4.27380.26541400.17712554269495
4.2738-5.38250.19891430.15622642278598
5.3825-40.48960.1916990.168227882887100
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)
13.0547-0.38471.13513.07292.00335.47090.2311-0.211-0.1706-0.0082-0.08720.0180.02640.2483-0.25390.3013-0.11910.00990.2865-0.00150.5352-14.0483-35.42544.5809
23.1778-0.04580.58351.5084-0.89442.13570.19090.20190.0643-0.0166-0.05390.2517-0.2331-0.1499-0.08090.34630.0334-0.01820.2892-0.08570.672-20.3761-26.1149-3.2291
34.73141.8404-2.22091.7751-1.36994.93840.15450.55080.2013-0.00040.02920.71920.2607-0.9072-0.16710.3576-0.0278-0.09110.3779-0.1250.744-35.6747-33.5973-2.4502
43.68370.3131-0.12891.7318-0.33181.14650.3563-0.7193-0.37830.3144-0.33950.31030.2285-0.1791-0.02510.4606-0.20970.05920.4402-0.03760.6337-24.6028-36.710112.1064
52.6061-1.45531.03231.5352-1.73252.26180.0325-0.15240.2893-0.044-0.1921-0.2789-0.008-0.1468-0.19060.4332-0.14470.0990.5146-0.26830.94256.4-2.636612.9899
61.75360.5346-0.31582.17030.78561.32520.1198-0.80710.5960.5504-0.26790.0183-0.17960.22390.15870.5398-0.21310.01130.673-0.16120.63276.206-13.943421.7742
70.26940.33610.80523.47051.79432.61410.1597-0.97310.78861.0436-0.46960.4009-0.1682-0.40050.21880.986-0.39790.01341.4405-0.60450.87035.8388-4.573237.5612
80.8754-0.16850.04781.14150.08431.286-0.1272-0.45590.36490.7271-0.1656-0.1363-0.0656-0.2485-0.56310.9848-0.50350.16291.4191-0.80430.607-4.5254-5.551733.7652
90.6136-0.29470.16460.52240.16370.59920.3453-0.73531.1560.3919-0.31270.1675-0.224-0.31590.07620.5925-0.2480.20050.7808-0.47121.0346-9.8305-9.466920.8085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 41 )A-2 - 41
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 135 )A42 - 135
3X-RAY DIFFRACTION3chain 'A' and (resid 136 through 202 )A136 - 202
4X-RAY DIFFRACTION4chain 'A' and (resid 203 through 345 )A203 - 345
5X-RAY DIFFRACTION5chain 'B' and (resid -2 through 15 )B-2 - 15
6X-RAY DIFFRACTION6chain 'B' and (resid 16 through 185 )B16 - 185
7X-RAY DIFFRACTION7chain 'B' and (resid 186 through 223 )B186 - 223
8X-RAY DIFFRACTION8chain 'B' and (resid 224 through 277 )B224 - 277
9X-RAY DIFFRACTION9chain 'B' and (resid 278 through 345 )B278 - 345

+
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