[English] 日本語
Yorodumi
- PDB-7s6f: Crystal structure of UrtA1 from Synechococcus WH8102 in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7s6f
TitleCrystal structure of UrtA1 from Synechococcus WH8102 in complex with urea and calcium
ComponentsPutative urea ABC transporter, urea binding protein
KeywordsTRANSPORT PROTEIN / Substrate-binding protein / marine cyanobacteria / urea-binding protein
Function / homology
Function and homology information


Urea ABC transporter, substrate-binding protein UrtA-like / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UREA / Putative urea ABC transporter, urea binding protein
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsShah, B.S. / Mikolajek, H. / Orr, C.M. / Mykhaylyk, V. / Owens, R.J. / Paulsen, I.T.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP200102944 Australia
Australian Research Council (ARC)CE200100029 Australia
CitationJournal: To Be Published
Title: Crystal structure of UrtA1 from Synechococcus WH8102 in complex with urea and calcium
Authors: Shah, B.S. / Mikolajek, H. / Orr, C.M. / Mykhaylyk, V. / Owens, R. / Paulsen, I.T.
History
DepositionSep 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative urea ABC transporter, urea binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8549
Polymers44,4691
Non-polymers3858
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.510, 71.390, 120.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-507-

CA

-
Components

#1: Protein Putative urea ABC transporter, urea binding protein


Mass: 44469.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (strain WH8102) (bacteria)
Strain: WH8102 / Gene: urtA1, SYNW2442 / Plasmid: pOPINM / Details (production host): Addgene Plasmid #26044 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: Q7U3J0
#2: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05 M Sodium Hepes: MOPS pH 7.5, 0.03 MgCl2, 0.03 CaCl2; 20 % PEG 500 MME; 10 % Peg 20000 Cryo: 30 % Ethylene Glycol

-
Data collection

DiffractionMean temperature: 50 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.7552 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Feb 27, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7552 Å / Relative weight: 1
ReflectionResolution: 1.8→120.46 Å / Num. obs: 35399 / % possible obs: 91.3 % / Redundancy: 38.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.032 / Rrim(I) all: 0.16 / Net I/σ(I): 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
9-120.46530.093206220.9990.0160.09599.9
1.8-1.8412.52.902213520.1611.1223.13976

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.8→71.492 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.849 / SU ML: 0.084 / Cross valid method: FREE R-VALUE / ESU R: 0.122 / ESU R Free: 0.113
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1903 1775 5.02 %
Rwork0.159 33583 -
all0.161 --
obs-35358 91.131 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.343 Å2
Baniso -1Baniso -2Baniso -3
1-0.777 Å2-0 Å20 Å2
2--0.797 Å2-0 Å2
3----1.574 Å2
Refinement stepCycle: LAST / Resolution: 1.8→71.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3064 0 17 263 3344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133148
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172891
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.6454267
X-RAY DIFFRACTIONr_angle_other_deg1.4091.5826705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9135394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7625.436149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11315516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.763155
X-RAY DIFFRACTIONr_chiral_restr0.0850.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023609
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02681
X-RAY DIFFRACTIONr_nbd_refined0.20.2598
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.22662
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21514
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21375
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2216
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0150.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1060.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1270.28
X-RAY DIFFRACTIONr_nbd_other0.1580.220
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2280.219
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0120.21
X-RAY DIFFRACTIONr_mcbond_it2.2993.3131580
X-RAY DIFFRACTIONr_mcbond_other2.2983.3131578
X-RAY DIFFRACTIONr_mcangle_it2.8544.961972
X-RAY DIFFRACTIONr_mcangle_other2.8544.9611973
X-RAY DIFFRACTIONr_scbond_it3.5313.6221568
X-RAY DIFFRACTIONr_scbond_other3.533.6221569
X-RAY DIFFRACTIONr_scangle_it5.095.2962295
X-RAY DIFFRACTIONr_scangle_other5.0895.2962296
X-RAY DIFFRACTIONr_lrange_it5.89739.3493559
X-RAY DIFFRACTIONr_lrange_other5.86239.0423513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.283850.3182092X-RAY DIFFRACTION77.6391
1.847-1.8970.2461060.252230X-RAY DIFFRACTION84.6991
1.897-1.9520.2411220.2292194X-RAY DIFFRACTION86.5794
1.952-2.0120.2981070.2212145X-RAY DIFFRACTION86.3828
2.012-2.0780.2371200.1852079X-RAY DIFFRACTION87.1236
2.078-2.1510.182990.172097X-RAY DIFFRACTION88.835
2.151-2.2330.2081020.152003X-RAY DIFFRACTION89.4983
2.233-2.3240.2271060.1551960X-RAY DIFFRACTION90.8132
2.324-2.4270.1891120.1361885X-RAY DIFFRACTION91.1456
2.427-2.5450.19950.1361857X-RAY DIFFRACTION92.6436
2.545-2.6830.206880.1491795X-RAY DIFFRACTION94.3387
2.683-2.8460.192880.1331720X-RAY DIFFRACTION95.208
2.846-3.0420.1761000.1441635X-RAY DIFFRACTION97.1445
3.042-3.2860.2091010.1541565X-RAY DIFFRACTION99.0488
3.286-3.5990.166730.1631493X-RAY DIFFRACTION99.9362
3.599-4.0230.173980.1451302X-RAY DIFFRACTION100
4.023-4.6450.194600.1351188X-RAY DIFFRACTION100
4.645-5.6870.175520.1721034X-RAY DIFFRACTION100
5.687-8.0330.231330.179822X-RAY DIFFRACTION100

+
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