[English] 日本語
Yorodumi
- PDB-3qec: Crystal structure of a putative carbohydrate binding protein (PA1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qec
TitleCrystal structure of a putative carbohydrate binding protein (PA1324) from Pseudomonas aeruginosa at 2.61 A resolution
ComponentsPutative carbohydrate binding protein
KeywordsCARBOHYDRATE-BINDING PROTEIN / SURAMIN BINDING / HEPARIN BINDING / POSSIBLE CARBOHYDRATE TRANSPORTER / BIOFILM FORMATION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY / CARBOHYDRATE- BINDING PROTEIN
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Carboxypeptidase regulatory-like domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.61 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative carbohydrate binding protein (PA1324) from Pseudomonas aeruginosa at 2.61 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Feb 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: Putative carbohydrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9797
Polymers16,3371
Non-polymers6436
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative carbohydrate binding protein
hetero molecules

A: Putative carbohydrate binding protein
hetero molecules

A: Putative carbohydrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,93821
Polymers49,0103
Non-polymers1,92818
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9110 Å2
ΔGint-34 kcal/mol
Surface area21580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.787, 132.787, 132.787
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-200-

SO4

21A-200-

SO4

DetailsCRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIC FORM.

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Putative carbohydrate binding protein


Mass: 16336.757 Da / Num. of mol.: 1 / Fragment: sequence database residues 22-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA1324 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9I420

-
Non-polymers , 5 types, 45 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE CONSTRUCT (RESIDUES 22-170) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 22-170) 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 15.00% Glycerol, 1.85% polyethylene glycol 400, 2.10M ammonium sulfate, 0.1M HEPES pH 7.9, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.98012,0.97944
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 23, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.980121
30.979441
ReflectionResolution: 2.61→29.692 Å / Num. obs: 12763 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 84.108 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 28.75
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.59-2.680.7842.8175891793177.5
2.68-2.790.6074.12783124051100
2.79-2.920.3596.7279282415199.9
2.92-3.070.2410268012312199.9
3.07-3.260.14316.3270232328199.9
3.26-3.510.08426.8270602341199.9
3.51-3.860.05838.1270552350199.8
3.86-4.420.04450.8271722379199.9
4.42-5.540.034602658223411100
5.54-29.6920.02765.3275982415199

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
SOLVEphasing
BUSTER-TNTBUSTER 2.8.0refinement
XSCALEdata processing
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.61→29.692 Å / Cor.coef. Fo:Fc: 0.9345 / Cor.coef. Fo:Fc free: 0.9339 / Occupancy max: 1 / Occupancy min: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0
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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. SULFATE (SO4) AND PEG-400 FRAGMENTS (PEG AND PGE) FROM THE CRYSTALLIZATION SOLUTION AND GLYCEROL FROM THE CRYOPROTECTANT HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 620 4.89 %RANDOM
Rwork0.2099 ---
obs0.2106 12685 --
Displacement parametersBiso max: 156.18 Å2 / Biso mean: 70.3766 Å2 / Biso min: 45.68 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.61→29.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1105 0 41 39 1185
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d531SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes33HARMONIC2
X-RAY DIFFRACTIONt_gen_planes172HARMONIC5
X-RAY DIFFRACTIONt_it1186HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion157SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1213SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1186HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1611HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion2.68
LS refinement shellResolution: 2.61→2.86 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2537 158 5.37 %
Rwork0.2278 2784 -
all0.2292 2942 -
Refinement TLS params.Method: refined / Origin x: 108.969 Å / Origin y: 133.414 Å / Origin z: 125.085 Å
111213212223313233
T-0.0445 Å20.1061 Å20.0076 Å2-0.0098 Å2-0.0235 Å2---0.1579 Å2
L1.4696 °2-0.2151 °20.1295 °2-2.3162 °2-1.1362 °2--1.8271 °2
S-0.024 Å °-0.0886 Å °0.0767 Å °0.0269 Å °0.1259 Å °0.148 Å °-0.3733 Å °-0.4312 Å °-0.1019 Å °

+
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