[English] 日本語
Yorodumi
- PDB-4otz: The crystal structure of a solute-binding protein (N280D mutant) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4otz
TitleThe crystal structure of a solute-binding protein (N280D mutant) from Anabaena variabilis ATCC 29413 in complex with cystein
ComponentsAmino acid/amide ABC transporter substrate-binding protein, HAAT family
KeywordsTRANSPORT PROTEIN / structural genomics / PSI-Biology / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


: / Leucine-binding protein domain / Periplasmic binding protein / 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
CYSTEINE / Amino acid/amide ABC transporter substrate-binding protein, HAAT family
Similarity search - Component
Biological speciesAnabaena variabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsTan, K. / Li, H. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a solute-binding protein (N280D mutant) from Anabaena variabilis ATCC 29413 in complex with cystein
Authors: Tan, K. / Li, H. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionFeb 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Amino acid/amide ABC transporter substrate-binding protein, HAAT family
B: Amino acid/amide ABC transporter substrate-binding protein, HAAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0206
Polymers84,7292
Non-polymers2914
Water14,106783
1
A: Amino acid/amide ABC transporter substrate-binding protein, HAAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5103
Polymers42,3641
Non-polymers1452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Amino acid/amide ABC transporter substrate-binding protein, HAAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5103
Polymers42,3641
Non-polymers1452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.738, 100.952, 150.458
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
11A-832-

HOH

21A-997-

HOH

-
Components

#1: Protein Amino acid/amide ABC transporter substrate-binding protein, HAAT family


Mass: 42364.367 Da / Num. of mol.: 2 / Mutation: N280D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis (bacteria) / Strain: ATCC 29413 / Gene: Ava_0465 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q3MFZ5
#2: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 783 / 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Original crystallization condition: 0.2 M Potassium Chloride, 20% (w/v) PEG 3350, 10mM valine. Crystal soaking condition: 0.2 M Potassium Chloride, 20% (w/v) PEG 3350, 10mM cystein, pH 7.0, ...Details: Original crystallization condition: 0.2 M Potassium Chloride, 20% (w/v) PEG 3350, 10mM valine. Crystal soaking condition: 0.2 M Potassium Chloride, 20% (w/v) PEG 3350, 10mM cystein, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97883 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2013 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97883 Å / Relative weight: 1
ReflectionResolution: 1.36→26 Å / Num. all: 158080 / Num. obs: 158080 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 5.9 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 31.3
Reflection shellResolution: 1.36→1.38 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 1.6 / Num. unique all: 6673 / % possible all: 83.8

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 4NQR

4nqr


Resolution: 1.36→25.847 Å / SU ML: 0.12 / σ(F): 1.34 / Phase error: 15.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1666 7914 5.01 %random
Rwork0.1392 ---
obs0.1406 157966 98.6 %-
all-157966 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.36→25.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5474 0 16 783 6273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055713
X-RAY DIFFRACTIONf_angle_d1.0447787
X-RAY DIFFRACTIONf_dihedral_angle_d13.2162133
X-RAY DIFFRACTIONf_chiral_restr0.074914
X-RAY DIFFRACTIONf_plane_restr0.0051034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3601-1.37560.28252000.23623987X-RAY DIFFRACTION80
1.3756-1.39180.25912490.22884404X-RAY DIFFRACTION88
1.3918-1.40870.27422520.21324765X-RAY DIFFRACTION94
1.4087-1.42660.23092650.19444888X-RAY DIFFRACTION98
1.4266-1.44530.20672920.17815049X-RAY DIFFRACTION100
1.4453-1.46510.20352530.16555009X-RAY DIFFRACTION100
1.4651-1.48610.19812790.15145036X-RAY DIFFRACTION100
1.4861-1.50820.18633110.14354995X-RAY DIFFRACTION100
1.5082-1.53180.18482620.13065049X-RAY DIFFRACTION100
1.5318-1.55690.16112590.12364989X-RAY DIFFRACTION100
1.5569-1.58380.15842480.12085096X-RAY DIFFRACTION100
1.5838-1.61260.16622390.11835066X-RAY DIFFRACTION100
1.6126-1.64360.15722680.11715066X-RAY DIFFRACTION100
1.6436-1.67710.17652520.11335064X-RAY DIFFRACTION100
1.6771-1.71360.15952690.11115038X-RAY DIFFRACTION100
1.7136-1.75340.15242650.11435029X-RAY DIFFRACTION100
1.7534-1.79730.15052480.11375081X-RAY DIFFRACTION100
1.7973-1.84580.14242820.11855027X-RAY DIFFRACTION100
1.8458-1.90010.18162690.12275066X-RAY DIFFRACTION100
1.9001-1.96140.16792650.12265095X-RAY DIFFRACTION100
1.9614-2.03150.15582450.12455078X-RAY DIFFRACTION100
2.0315-2.11280.15742540.12125096X-RAY DIFFRACTION100
2.1128-2.20890.15842750.1265084X-RAY DIFFRACTION100
2.2089-2.32530.15532780.13345033X-RAY DIFFRACTION100
2.3253-2.47090.1542560.13795137X-RAY DIFFRACTION100
2.4709-2.66150.15532670.14325103X-RAY DIFFRACTION100
2.6615-2.9290.17992890.1515107X-RAY DIFFRACTION100
2.929-3.35210.19132550.1565170X-RAY DIFFRACTION100
3.3521-4.22030.14332930.14065167X-RAY DIFFRACTION100
4.2203-25.85170.1662750.14535278X-RAY DIFFRACTION99

+
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