[English] 日本語
Yorodumi
- PDB-4dxc: Crystal structure of the engineered MBP TEM-1 fusion protein RG13... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dxc
TitleCrystal structure of the engineered MBP TEM-1 fusion protein RG13, C2 space group
ComponentsMaltose-binding periplasmic protein, Beta-lactamase TEM chimera
KeywordsSUGAR BINDING PROTEIN / HYDROLASE / TEM / beta-lactamase / MBP / allosteric regulation / zinc binding / maltose binding
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / beta-lactam antibiotic catabolic process / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / beta-lactam antibiotic catabolic process / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / periplasmic space / response to antibiotic / DNA damage response / membrane
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein ...Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Periplasmic binding protein-like II / Beta-lactamase/transpeptidase-like / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
Authorsvan den Akker, F. / Ke, W.
CitationJournal: Plos One / Year: 2012
Title: Structure of an Engineered beta-Lactamase Maltose Binding Protein Fusion Protein: Insights into Heterotropic Allosteric Regulation.
Authors: Ke, W. / Laurent, A.H. / Armstrong, M.D. / Chen, Y. / Smith, W.E. / Liang, J. / Wright, C.M. / Ostermeier, M. / van den Akker, F.
History
DepositionFeb 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Sep 13, 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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.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_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 1.3Nov 27, 2024Group: Structure summary / Category: 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: Maltose-binding periplasmic protein, Beta-lactamase TEM chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0683
Polymers69,9371
Non-polymers1312
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.450, 47.844, 108.288
Angle α, β, γ (deg.)90.00, 114.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-914-

HOH

-
Components

#1: Protein Maltose-binding periplasmic protein, Beta-lactamase TEM chimera / RG13


Mass: 69937.273 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: malE, bla / Production host: Escherichia coli (E. coli) / Strain (production host): malE- auxotroph PM9F'
References: UniProt: P0AEX9, UniProt: P62593, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRG13 IS A CHIMERA COMPRISING THE N-TERMINAL DOMAIN OF MALTOSE-BINDING PERIPLASMIC PROTEIN (UNP ...RG13 IS A CHIMERA COMPRISING THE N-TERMINAL DOMAIN OF MALTOSE-BINDING PERIPLASMIC PROTEIN (UNP RESIDUES 27-342), THE C-TERMINAL DOMAIN OF BETA-LACTAMASE TEM (UNP RESIDUES 227-286), AN ENGINEERED LINKER (GSGGG), THE N-TERMINAL DOMAIN OF BETA-LACTAMASE TEM (UNP RESIDUES 24-226), AN ENGINEERED LINKER (S), AND THE C-TERMINAL DOMAIN OF MALTOSE-BINDING PERIPLASMIC PROTEIN (UNP RESIDUES 345-396).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: A 1.0 uL drop was prepared using 0.5 uL protein mixture (13.8 mg/mL RG13, 2.5 mM zinc chloride) and 0.5 uL reservoir solution (0.2 M ammonium acetate, 0.1 M Tris, pH 8.5-9.5, 15-30% PEG3350) ...Details: A 1.0 uL drop was prepared using 0.5 uL protein mixture (13.8 mg/mL RG13, 2.5 mM zinc chloride) and 0.5 uL reservoir solution (0.2 M ammonium acetate, 0.1 M Tris, pH 8.5-9.5, 15-30% PEG3350) and equilibrated over a 1 ml reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.081 / Wavelength: 1.081 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2007 / Details: mirrors
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0811
21.0811
ReflectionResolution: 2.3→42.32 Å / Num. all: 26202 / Num. obs: 23194 / % possible obs: 49.95 % / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Biso Wilson estimate: 41.958 Å2 / Rmerge(I) obs: 0.051
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.051 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2258 / % possible all: 88.2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1ZG4 AND 1OMP

1zg4

1omp


Resolution: 2.3→42.32 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.896 / SU B: 9.472 / SU ML: 0.234 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.863 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29097 1182 5.1 %RANDOM
Rwork0.23289 ---
obs0.23593 22012 88.52 %-
all-22805 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.916 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.02 Å2
2--0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4830 0 2 134 4966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224930
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9421.9716683
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7055621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3325.023213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71615856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3921524
X-RAY DIFFRACTIONr_chiral_restr0.0630.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213713
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_it0.4471.53100
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82824977
X-RAY DIFFRACTIONr_scbond_it0.94431830
X-RAY DIFFRACTIONr_scangle_it1.6084.51706
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 93 -
Rwork0.278 1473 -
obs--82.73 %

+
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