[English] 日本語
Yorodumi
- PDB-3ocr: Crystal structure of aldolase II superfamily protein from Pseudom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ocr
TitleCrystal structure of aldolase II superfamily protein from Pseudomonas syringae
ComponentsClass II aldolase/adducin domain protein
KeywordsLYASE / PSI-2 / Midwest Center for Structural Genomics / Protein Structure Initiative / MCSG
Function / homology
Function and homology information


monosaccharide metabolic process / actin filament binding / cytoskeleton
Similarity search - Function
: / L-fuculose-1-phosphate Aldolase / Class II aldolase/adducin N-terminal domain / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Class II aldolase/adducin domain protein
Similarity search - Component
Biological speciesPseudomonas syringae pv. phaseolicola 1448A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsChang, C. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of aldolase II superfamily protein from Pseudomonas syringae
Authors: Chang, C. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionAug 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Class II aldolase/adducin domain protein
B: Class II aldolase/adducin domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5743
Polymers59,4782
Non-polymers961
Water6,035335
1
A: Class II aldolase/adducin domain protein

A: Class II aldolase/adducin domain protein

A: Class II aldolase/adducin domain protein

A: Class II aldolase/adducin domain protein


Theoretical massNumber of molelcules
Total (without water)118,9574
Polymers118,9574
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area11150 Å2
ΔGint-43 kcal/mol
Surface area37160 Å2
MethodPISA
2
B: Class II aldolase/adducin domain protein
hetero molecules

B: Class II aldolase/adducin domain protein
hetero molecules

B: Class II aldolase/adducin domain protein
hetero molecules

B: Class II aldolase/adducin domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,3418
Polymers118,9574
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area10670 Å2
ΔGint-82 kcal/mol
Surface area37360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.407, 74.407, 179.909
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-334-

HOH

21A-353-

HOH

31B-290-

HOH

41B-335-

HOH

51B-351-

HOH

-
Components

#1: Protein Class II aldolase/adducin domain protein


Mass: 29739.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. phaseolicola 1448A (bacteria)
Strain: 1448A / Race 6 / Gene: PSPPH_2884 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)gold / References: UniProt: Q48HR6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.24 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG4K 30%, Ammonium Acetate 0.2M, tri-Na-Citrate 0.1M, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 37960 / Num. obs: 37674 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 11.5 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 40.4
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.665 / Num. unique all: 1808 / % possible all: 98.6

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
RESOLVEphasing
Cootmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 9.405 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.167
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 1882 5 %RANDOM
Rwork0.183 ---
all0.1858 39490 --
obs0.1858 37608 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 94.32 Å2 / Biso mean: 35.437 Å2 / Biso min: 18.26 Å2
Baniso -1Baniso -2Baniso -3
1--2.62 Å20 Å20 Å2
2---2.62 Å20 Å2
3---5.23 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 5 335 4192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214174
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9355706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4165543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99323.204206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48715658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9211538
X-RAY DIFFRACTIONr_chiral_restr0.0890.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213300
X-RAY DIFFRACTIONr_mcbond_it1.3551.52614
X-RAY DIFFRACTIONr_mcangle_it2.44224208
X-RAY DIFFRACTIONr_scbond_it2.53531560
X-RAY DIFFRACTIONr_scangle_it4.154.51498
X-RAY DIFFRACTIONr_rigid_bond_restr1.36434174
LS refinement shellResolution: 1.947→1.997 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 109 -
Rwork0.215 2491 -
all-2600 -
obs-2600 98.34 %
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)
10.40350.05980.08260.2880.04670.0867-0.00610.0136-0.0016-0.01780.00390.02310.00120.00870.00220.2215-0.0021-0.00060.2186-0.00040.202711.0898.71959.281
20.0895-0.03980.03380.07640.00190.0111-0.0001-0.00270.01170.003-0.00750.01170.005-0.00080.00760.2191-0.00060.00150.22-0.00080.204520.6213.78679.101
30.24040.3837-0.02910.96810.41280.6648-0.06670.11690.0916-0.07310.0940.02240.0144-0.0166-0.02730.225-0.0204-0.01220.26420.03420.210225.64317.41656.763
40.41640.18520.26830.6729-0.24720.6198-0.0328-0.05190.09310.0462-0.0018-0.008-0.0441-0.05640.03460.22770.0114-0.00320.2298-0.01130.177120.45322.03129.406
50.0744-0.1051-0.01890.1293-0.00780.0041-0.00680.00110.0115-0.00320.0030.0194-0.0034-0.00780.00380.2205-0.0002-0.00060.22160.00010.19619.6612.1919.757
60.20330.208-0.14420.83010.3360.38620.035-0.0154-0.03110.019-0.0217-0.025-0.0196-0.0271-0.01340.21770.0013-0.00320.2294-0.00150.191116.8295.48832.316
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 105
2X-RAY DIFFRACTION2A106 - 246
3X-RAY DIFFRACTION3A247 - 271
4X-RAY DIFFRACTION4B1 - 105
5X-RAY DIFFRACTION5B106 - 246
6X-RAY DIFFRACTION6B247 - 271

+
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