[English] 日本語
Yorodumi
- PDB-2w7z: Structure of the pentapeptide repeat protein EfsQnr, a DNA gyrase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2w7z
TitleStructure of the pentapeptide repeat protein EfsQnr, a DNA gyrase inhibitor. Free amines modified by cyclic pentylation with glutaraldehyde.
ComponentsPENTAPEPTIDE REPEAT FAMILY PROTEIN
KeywordsINHIBITOR / GLUTARALDEHYDE / GYRASE INHIBITOR / CYCLIC PENTYLATION / CHEMICAL MODIFICATION / PENTAPEPTIDE REPEAT PROTEIN
Function / homology: / Pentapeptide repeat region / Pentapeptide repeats (8 copies) / Pentapeptide repeat / E3 ubiquitin-protein ligase SopA / Pectate Lyase C-like / 3 Solenoid / Mainly Beta / Pentapeptide repeat family protein
Function and homology information
Biological speciesENTEROCOCCUS FAECALIS (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.6 Å
AuthorsVetting, M.W. / Hegde, S.S. / Blanchard, J.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Crystallization of a Pentapeptide-Repeat Protein by Reductive Cyclic Pentylation of Free Amines with Glutaraldehyde.
Authors: Vetting, M.W. / Hegde, S.S. / Blanchard, J.S.
History
DepositionJan 6, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PENTAPEPTIDE REPEAT FAMILY PROTEIN
B: PENTAPEPTIDE REPEAT FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1896
Polymers50,0472
Non-polymers1424
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-32.4 kcal/mol
Surface area23330 Å2
MethodPQS
Unit cell
Length a, b, c (Å)36.930, 63.139, 94.619
Angle α, β, γ (deg.)90.00, 96.09, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8509, -0.5237, -0.04045), (-0.5206, 0.8306, 0.1976), (-0.06988, 0.1892, -0.9795)
Vector: 2.741, -7.347, 81.33)

-
Components

#1: Protein PENTAPEPTIDE REPEAT FAMILY PROTEIN / EFSQNR


Mass: 25023.357 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CHEMICAL MODIFICATION OF THE FREE AMINES (LYSINES, N-TERMINUS) BY TREATMENT WITH GLUTARALDEHYDE UNDER REDUCING CONDITIONS
Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q837D8
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsLYSYL-PIPERIDINE (LPD): UNSATURATED SIX-MEMBERED RING, WITH PROTONATED NITROGEN, SP3 GEOMETRY, AND ...LYSYL-PIPERIDINE (LPD): UNSATURATED SIX-MEMBERED RING, WITH PROTONATED NITROGEN, SP3 GEOMETRY, AND FIVE CARBONS, A PIPERIDINE GROUP ON LYSINE SIDE CHAIN.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.14 % / Description: NONE
Crystal growpH: 6
Details: PROTEIN - 10 MG/ML, 400 MM AMMONIUM SULFATE, 15 MM HEPES PH 7.5, 1 MM DTT, 1 MM ETDA PRECIPITANT - 100 MM MES PH 6.5, 5-15% PEG 6000, 1M LICL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU R-AXIS IV / Date: Jan 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→20.6 Å / Num. obs: 53909 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.1 / % possible all: 86

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.6→94.07 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.462 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PROTEIN WAS PRODUCED WITH N-TERMINAL THROMBIN CLEAVABLE TAG. PROTEIN WAS CRYSTALLIZED AFTER THROMBIN CLEAVAGE, LEAVING A NON-NATIVE N-TERMINUS OF GLYSERHIS-MET1
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2736 5.1 %RANDOM
Rwork0.19 ---
obs0.192 51172 94.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.34 Å2
2--0.63 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.6→94.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 4 417 3855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223592
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9734894
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8945426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41224.787188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.74615511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2181516
X-RAY DIFFRACTIONr_chiral_restr0.0940.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022756
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21643
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.22495
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7151.52172
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09323430
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0331594
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.144.51464
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.446 193
Rwork0.367 3093
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9280.25950.43630.58340.22561.99080.00080.0298-0.03870.07970.0099-0.07070.07310.0532-0.01080.01610.0386-0.01680.01740.00090.008722.4114.31474.259
21.54910.1410.77981.2640.42292.26740.04220.075-0.0746-0.0336-0.0297-0.00140.127-0.0584-0.01250.03080.0229-0.0020.0573-0.01770.020112.5560.76959.435
31.3880.91631.63160.80150.98193.08390.02550.1294-0.0266-0.04830.0069-0.04930.07790.0232-0.03240.01070.0154-0.00610.0787-0.0404-0.00425.391-3.88247.041
41.01330.03040.04951.79280.43311.8804-0.0281-0.00920.0517-0.43450.06550.2231-0.3038-0.0039-0.03750.1194-0.035-0.032-0.04080.02890.0028-21.332-0.3636.923
50.92740.13070.61881.5370.34621.9092-0.0107-0.08870.012-0.02570.109-0.0334-0.15030.0975-0.09830.024-0.0270.03870.0572-0.00980.021-11.122-2.19723.612
61.0759-0.03410.51650.167-0.52692.27250.063-0.07070.06520.1040.0071-0.01160.02210.1284-0.07020.01560.0046-0.00130.1065-0.06120.01820.172-3.49635.425
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 114
2X-RAY DIFFRACTION2A115 - 168
3X-RAY DIFFRACTION3A169 - 211
4X-RAY DIFFRACTION4B4 - 109
5X-RAY DIFFRACTION5B110 - 180
6X-RAY DIFFRACTION6B181 - 211

+
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