[English] 日本語
Yorodumi
- PDB-3gmy: Crystal Structure of Beta-Lactamse Inhibitory Protein-Like Protei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gmy
TitleCrystal Structure of Beta-Lactamse Inhibitory Protein-Like Protein (BLP), Selenomethionine Derivative
ComponentsBLP
KeywordsPROTEIN BINDING / 2-layer alpha/beta sandwich
Function / homologyBLIP domain / Beta-lactamase-inhibitor protein BLIP / Beta-lactamase-inhibitor protein BLIP domain superfamily / Beta-lactamase inhibitor (BLIP) / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Beta-Lactamase Inhibitory Protein-Like Protein / Beta-Lactamase Inhibitory Protein-Like Protein
Function and homology information
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsGretes, M. / Strynadka, N.C.J.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Insights into positive and negative requirements for protein-protein interactions by crystallographic analysis of the beta-lactamase inhibitory proteins BLIP, BLIP-I, and BLP.
Authors: Gretes, M. / Lim, D.C. / de Castro, L. / Jensen, S.E. / Kang, S.G. / Lee, K.J. / Strynadka, N.C.
History
DepositionMar 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BLP
B: BLP


Theoretical massNumber of molelcules
Total (without water)35,4802
Polymers35,4802
Non-polymers00
Water8,629479
1
A: BLP


Theoretical massNumber of molelcules
Total (without water)17,7401
Polymers17,7401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BLP


Theoretical massNumber of molelcules
Total (without water)17,7401
Polymers17,7401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.167, 67.195, 41.208
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein BLP


Mass: 17740.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Strain: ATCC 27064 / Gene: blp / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P97062, UniProt: B5GLC0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.68 %
Crystal growTemperature: 294 K / Method: hanging drop / pH: 8.5
Details: 11 mg/ml protein in 30 mM tris, 150 mM NaCl mixed 1:1 with well solution 30% PEG 4000, 0.2 M sodium acetate trihydrate, pH 8.5, hanging drop, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Feb 27, 2006
RadiationMonochromator: DOUBLE CRYSTAL SILICON (111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionRedundancy: 5.7 % / Av σ(I) over netI: 45.17 / Number: 171171 / Rmerge(I) obs: 0.077 / Χ2: 4.07 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 30061 / % possible obs: 94.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.665084.110.06810.0725.5
2.913.669210.065.5225.6
2.542.9195.810.0735.1665.8
2.312.5497.410.0814.5265.8
2.142.3193.310.0863.5295.2
2.022.1496.310.0863.4375.9
1.912.0296.710.1083.0575.8
1.831.9196.710.1342.3995.8
1.761.8396.510.1431.9955.8
1.71.7696.110.1671.7025.8
ReflectionResolution: 1.7→55.99 Å / Num. obs: 30474 / % possible obs: 96.5 % / Redundancy: 7.6 % / Rsym value: 0.084 / Net I/σ(I): 34.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 7.9 % / Rsym value: 0.23 / % possible all: 96.2

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→55 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.84 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 5.93 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.321 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1598 5 %RANDOM
Rwork0.2 ---
obs0.20328 30103 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.042 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å2-0 Å2
2--0.33 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.7→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 0 0 479 2965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222569
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.091.9343503
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9465312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.18923.893131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55815394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8311516
X-RAY DIFFRACTIONr_chiral_restr0.1410.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212052
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2490.31344
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.51777
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.5602
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2860.366
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2770.560
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.26721557
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.05532518
X-RAY DIFFRACTIONr_scbond_it2.69621012
X-RAY DIFFRACTIONr_scangle_it3.4783982
X-RAY DIFFRACTIONr_rigid_bond_restr2.11132569
X-RAY DIFFRACTIONr_sphericity_free8.3973479
X-RAY DIFFRACTIONr_sphericity_bonded3.78332486
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 127 -
Rwork0.174 2171 -
obs--100 %

+
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