[English] 日本語
Yorodumi
- PDB-3os7: Crystal structure of a galactose mutarotase-like protein (CA_C069... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3os7
TitleCrystal structure of a galactose mutarotase-like protein (CA_C0697) from CLOSTRIDIUM ACETOBUTYLICUM at 1.80 A resolution
Componentsgalactose mutarotase-like protein
KeywordsISOMERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


isomerase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Aldose 1-/Glucose-6-phosphate 1-epimerase / Aldose 1-epimerase / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Galactose mutarotase related enzyme
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a galactose mutarotase-like protein (CA_C0697) from CLOSTRIDIUM ACETOBUTYLICUM at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Aug 8, 2012Group: Data collection
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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: galactose mutarotase-like protein
B: galactose mutarotase-like protein
C: galactose mutarotase-like protein
D: galactose mutarotase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,95034
Polymers156,8114
Non-polymers3,13930
Water30,4271689
1
A: galactose mutarotase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9277
Polymers39,2031
Non-polymers7256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: galactose mutarotase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,98110
Polymers39,2031
Non-polymers7799
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: galactose mutarotase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,11410
Polymers39,2031
Non-polymers9119
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: galactose mutarotase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9277
Polymers39,2031
Non-polymers7256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)209.532, 41.553, 211.641
Angle α, β, γ (deg.)90.000, 119.580, 90.000
Int Tables number5
Space group name H-MC121
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK: CRYSTAL PACKING AND ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

-
Components

#1: Protein
galactose mutarotase-like protein / Galactose mutarotase related enzyme


Mass: 39202.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Gene: CA_C0697 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q97L65
#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1689 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 22.2% polyethylene glycol 3350, 0.257M di-sodium tartrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL14-111
SYNCHROTRONSSRL BL9-220.97929,0.91837,0.97913
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDMay 26, 2010flat collimating mirror, toroidal focusing mirror
MARMOSAIC 325 mm CCD2CCDMar 11, 2010Flat collimating mirror, toroid focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal monochromator Si(111)SINGLE WAVELENGTHMx-ray1
2Double crystal monochromatorMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979291
30.918371
40.979131
ReflectionResolution: 1.8→29.553 Å / Num. obs: 146955 / % possible obs: 93.5 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 17.043 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 10.27
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.860.332237047225161,283.8
1.86-1.940.272356718288321,293.2
1.94-2.030.1814.555022274811,294
2.03-2.130.145.750864253931,294.1
2.13-2.270.1156.857286286021,294.5
2.27-2.440.0958.153201264781,294.3
2.44-2.690.0779.855430277771,295.3
2.69-3.070.05213.953766268691,295
3.07-3.870.03121.355063275851,294.8
3.87-29.5530.02526.155294278291,295.8

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.553 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.117 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.102
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. TARTRATE (TLA), ETHYLENE GLYCOL (EDO), AND POLY ETHYLENE GLYCOL (PG4) MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1808 7348 5 %RANDOM
Rwork0.1428 ---
obs0.1447 146955 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.46 Å2 / Biso mean: 21.3137 Å2 / Biso min: 4.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å2-0.18 Å2
2---0.12 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10863 0 195 1689 12747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02211752
X-RAY DIFFRACTIONr_bond_other_d0.0020.028280
X-RAY DIFFRACTIONr_angle_refined_deg1.461.96715911
X-RAY DIFFRACTIONr_angle_other_deg0.866320365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38751495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29625.328548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.384152151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0631538
X-RAY DIFFRACTIONr_chiral_restr0.0950.21704
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112978
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022292
X-RAY DIFFRACTIONr_mcbond_it1.75736985
X-RAY DIFFRACTIONr_mcbond_other0.51832804
X-RAY DIFFRACTIONr_mcangle_it2.961511431
X-RAY DIFFRACTIONr_scbond_it4.62384767
X-RAY DIFFRACTIONr_scangle_it7.126114411
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 491 -
Rwork0.224 9546 -
all-10037 -
obs--92.89 %
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)
10.26460.09990.17220.3017-0.06810.1825-0.0366-0.05290.0226-0.06370.0041-0.01830.0149-0.03660.03250.07160.04280.01780.04050.00420.0091-54.882338.7826133.6347
20.1730.05840.15590.2680.0270.21920.0036-0.03620.0235-0.02030.0176-0.02710.0183-0.035-0.02120.0148-0.0081-0.00040.0174-0.00830.042-99.931919.8544225.2584
30.0589-0.12870.13020.56840.1120.8991-0.0048-0.0343-0.0051-0.02430.0440.00250.0342-0.097-0.03910.0212-0.00450.00020.04110.00920.0158-81.864416.6695274.8941
40.10670.05170.13260.1923-0.09260.41710.02550.01590.02970.0033-0.03120.03690.0440.03380.00570.01980.00430.00980.0163-0.00120.0398-74.022918.5532180.1732
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 401
2X-RAY DIFFRACTION2B3 - 401
3X-RAY DIFFRACTION3C3 - 401
4X-RAY DIFFRACTION4D3 - 401

+
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://pdbjlvh1.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