[English] 日本語
Yorodumi
- PDB-4iab: Crystal structure of a putative monosaccharide binding protein (B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4iab
TitleCrystal structure of a putative monosaccharide binding protein (BACUNI_03039) from Bacteroides uniformis ATCC 8492 at 1.70 A resolution
Componentshypothetical protein
KeywordsStructural Genomics / Unknown Function / Lipocalin-like fold protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyDomain of unknown function DUF4488 / Domain of unknown function (DUF4488) / Uncharacterised protein PF14869 family, DUF4488 / Lipocalin / Beta Barrel / Mainly Beta / DI(HYDROXYETHYL)ETHER / Unknown ligand / DUF4488 domain-containing protein
Function and homology information
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.66 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACUNI_03039) from Bacteroides uniformis ATCC 8492 at 1.66 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 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: hypothetical protein
B: hypothetical protein
C: hypothetical protein
D: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,45114
Polymers65,8284
Non-polymers62310
Water11,313628
1
A: hypothetical protein
B: hypothetical protein
hetero molecules

A: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,64916
Polymers65,8284
Non-polymers82112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_567x,-y+1,-z+21
Buried area14680 Å2
ΔGint-66 kcal/mol
Surface area26920 Å2
MethodPISA
2
A: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3248
Polymers32,9142
Non-polymers4106
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-22 kcal/mol
Surface area15000 Å2
MethodPISA
3
C: hypothetical protein
D: hypothetical protein
hetero molecules

C: hypothetical protein
D: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,25212
Polymers65,8284
Non-polymers4248
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_657-x+1,y,-z+5/21
Buried area14690 Å2
ΔGint-56 kcal/mol
Surface area25170 Å2
MethodPISA
4
C: hypothetical protein
D: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1266
Polymers32,9142
Non-polymers2124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-22 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.731, 213.875, 153.643
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-385-

HOH

21C-362-

HOH

31D-372-

HOH

-
Components

#1: Protein
hypothetical protein /


Mass: 16456.980 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Strain: ATCC 8492 / Gene: ZP_02071597.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7V626
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#3: 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
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 628 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING GLY 0 FOLLOWED BY RESIDUES 23-163 OF THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.0M lithium chloride, 20.0% polyethylene glycol 6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979493,0.918401,0.979288
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2012 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9794931
20.9184011
30.9792881
ReflectionResolution: 1.66→46.19 Å / Num. obs: 84998 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.61 % / Biso Wilson estimate: 21.673 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 15.49
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.66-1.723.630.562.230742846998.9
1.72-1.793.670.3783.231599860599.9
1.79-1.873.680.2444.9305978313100
1.87-1.973.60.1577.730608849699
1.97-2.093.610.1041129619820498.7
2.09-2.253.660.07215.130763839899.5
2.25-2.483.650.0541931668867299.5
2.48-2.843.610.04423.530918855499.3
2.84-3.573.530.03130.930044850399
3.57-46.193.460.02536.330383878497

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
REFMAC5.7.0032refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.66→46.19 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 3.268 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.08
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. 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 ...Details: 1. 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. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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. UNKNOWN LIGANDS (UNL) WERE MODELED INTO THE PUTATIVE ACTIVE SITE ON EACH SUBUNIT. 7. POLYETHYLENE GLYCOL FRAGMENTS (PEG) FROM THE CRYSTALLIZATION SOLUTION AND GLYCEROL (GOL),USED AS A CRYOPROTECTANT, WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.18394 4249 5 %RANDOM
Rwork0.16262 ---
obs0.16369 80705 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.849 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å2-0 Å2
2---0.77 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.66→46.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4399 0 81 628 5108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194826
X-RAY DIFFRACTIONr_bond_other_d0.0010.024566
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.9766599
X-RAY DIFFRACTIONr_angle_other_deg0.737310602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3685625
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.01325.064233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13315776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5241516
X-RAY DIFFRACTIONr_chiral_restr0.0150.2711
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215498
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021102
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5343.1462277
X-RAY DIFFRACTIONr_mcbond_other2.5323.1452276
X-RAY DIFFRACTIONr_mcangle_it3.6585.8692864
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 320 -
Rwork0.248 5883 -
obs--98.62 %
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)
10.68190.24030.06381.4424-0.07751.8508-0.03640.04990.1446-0.12370.04530.1136-0.0271-0.0992-0.00890.01560.002-0.00590.02220.01780.046712.557897.2509134.9166
20.8027-0.04660.07561.3569-0.54531.43120.0422-0.06840.0697-0.0253-0.04730.05810.0374-0.01040.00510.0058-0.0020.01330.0278-0.00970.049518.943987.2735155.8001
30.84760.05770.12711.5526-0.34711.26820.0174-0.03780.02360.05580.00630.0163-00.0164-0.02370.04560.00290.01280.0420.0040.014124.412964.6529175.4556
40.8882-0.1737-0.22761.76570.04580.90450.0201-0.0081-0.0069-0.00590.0020.00480.0439-0.0425-0.0220.0764-0.0024-0.00180.0557-0.00030.025527.949742.1701176.6345
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 163
2X-RAY DIFFRACTION2B28 - 163
3X-RAY DIFFRACTION3C28 - 163
4X-RAY DIFFRACTION4D31 - 163

+
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