[English] 日本語
Yorodumi
- PDB-3ltb: X-ray structure of a non-biological ATP binding protein determine... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ltb
TitleX-ray structure of a non-biological ATP binding protein determined in the presence of 10 mM ATP at 2.6 A after 3 weeks of incubation
ComponentsATP BINDING PROTEIN-DX
KeywordsDE NOVO PROTEIN / ALPHA/BETA FOLD / BENT ATP / NON-BIOLOGICAL PROTEIN
Function / homologyNuclear Transport Factor 2; Chain: A, - #210 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / ADENOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSimmons, C.R. / Magee, C.L. / Allen, J.P. / Chaput, J.C.
CitationJournal: Biochemistry / Year: 2010
Title: Three-dimensional structures reveal multiple ADP/ATP binding modes for a synthetic class of artificial proteins.
Authors: Simmons, C.R. / Magee, C.L. / Smith, D.A. / Lauman, L. / Chaput, J.C. / Allen, J.P.
History
DepositionFeb 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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: ATP BINDING PROTEIN-DX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5557
Polymers9,7081
Non-polymers8466
Water61334
1
A: ATP BINDING PROTEIN-DX
hetero molecules

A: ATP BINDING PROTEIN-DX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,10914
Polymers19,4162
Non-polymers1,69312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area4220 Å2
ΔGint-47 kcal/mol
Surface area8200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.255, 72.255, 54.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein ATP BINDING PROTEIN-DX


Mass: 9708.112 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Description: THE ATP BINDING PROTEIN CONSTRUCT WAS DERIVED DE NOVO VIA DIRECTED EVOLUTION
Plasmid: PIADL14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

-
Non-polymers , 5 types, 40 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 71.13 %
Crystal growpH: 8.5
Details: 0.1 M SODIUM PHOSPHATE PH 8.5, 0.25 M SODIUM CITRATE, 0.3 M SODIUM CHLORIDE, 23% PEG 400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K

-
Data collection

DiffractionMean temperature: 143 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 6, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 5306 / % possible obs: 99.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 20.289
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.553 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G4B

3g4b
PDB Unreleased entry


Resolution: 2.6→20.63 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.891 / SU B: 6.706 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.24 243 4.6 %RANDOM
Rwork0.183 ---
obs0.185 5288 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms583 0 50 34 667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021645
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.992866
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.842568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.57523.22631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86515111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.192155
X-RAY DIFFRACTIONr_chiral_restr0.1020.286
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021463
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7651.5344
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.522559
X-RAY DIFFRACTIONr_scbond_it2.2423301
X-RAY DIFFRACTIONr_scangle_it3.6784.5307
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 14 -
Rwork0.227 364 -
obs--99.21 %

+
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