[English] 日本語
Yorodumi
- PDB-3l57: Crystal Structure of the Plasmid pCU1 TraI Relaxase Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3l57
TitleCrystal Structure of the Plasmid pCU1 TraI Relaxase Domain
ComponentsMobilization protein TraI
KeywordsHYDROLASE / TrwC superfamily of relaxase enzymes / conjugative relaxase / Mob class relaxase / conjugal nickase / histidine triad / HUH+H motif
Function / homology
Function and homology information


Conjugative relaxase, N-terminal / TrwC relaxase / TrwC relaxase / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CITRIC ACID / MANGANESE (III) ION / PHOSPHATE ION / TraI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.293 Å
AuthorsRedinbo, M.R. / Nash, R.P.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: The mechanism and control of DNA transfer by the conjugative relaxase of resistance plasmid pCU1.
Authors: Nash, R.P. / Habibi, S. / Cheng, Y. / Lujan, S.A. / Redinbo, M.R.
History
DepositionDec 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.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_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_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: Mobilization protein TraI
B: Mobilization protein TraI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,91432
Polymers67,9042
Non-polymers2,01130
Water3,945219
1
A: Mobilization protein TraI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,47323
Polymers33,9521
Non-polymers1,52122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mobilization protein TraI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4419
Polymers33,9521
Non-polymers4898
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.280, 58.520, 87.120
Angle α, β, γ (deg.)90.000, 83.880, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Mobilization protein TraI / / TraI


Mass: 33951.863 Da / Num. of mol.: 2 / Fragment: Relaxase Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pMUR050_047, traI / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9X4G2, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

-
Non-polymers , 5 types, 249 molecules

#2: Chemical ChemComp-MN3 / MANGANESE (III) ION / Manganese


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 1.88 Å3/Da / Density % sol: 34.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 250mM triNa citrate, 22% PEG 3350, 5mM MgCl2, vapor diffusion, hanging drop, temperature 293.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.999 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 1, 2008 / Details: Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock monochromator high-resolution double-crystal Si(220)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.29→49.999 Å / Num. all: 22781 / Num. obs: 22081 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 45.743 Å2 / Rsym value: 0.054 / Net I/σ(I): 18.25
Reflection shellResolution: 2.29→2.43 Å / Mean I/σ(I) obs: 4.5 / Num. measured obs: 12219 / Num. unique all: 3362 / Num. unique obs: 3362 / Rsym value: 0.401 / % possible all: 91.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.29 Å48.49 Å
Translation2.29 Å48.49 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER1.3.2phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
SERGUIdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1omh, Plasmid R388 TrwC Relaxase Domain

1omh


Resolution: 2.293→48.492 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.842 / SU ML: 0.08 / Isotropic thermal model: isotropic + TLS / Cross valid method: THROUGHOUT / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1105 5.01 %Random
Rwork0.173 ---
obs0.176 22077 96.97 %-
all-22781 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.392 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 107.69 Å2 / Biso mean: 47.255 Å2 / Biso min: 20.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å24.495 Å2
2---7.78 Å20 Å2
3---7.58 Å2
Refinement stepCycle: LAST / Resolution: 2.293→48.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3244 0 124 219 3587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033493
X-RAY DIFFRACTIONf_angle_d0.7244688
X-RAY DIFFRACTIONf_chiral_restr0.048527
X-RAY DIFFRACTIONf_plane_restr0.002604
X-RAY DIFFRACTIONf_dihedral_angle_d15.6861276
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.293-2.3980.2441320.20324992631249993
2.398-2.5240.2681360.20825922728259297
2.524-2.6820.2921370.20425982735259897
2.682-2.8890.2181380.18526222760262297
2.889-3.180.2451390.17326452784264598
3.18-3.640.241400.16426562796265698
3.64-4.5850.1981390.1426412780264197
4.585-48.5020.2011440.17527192863271998
Refinement TLS params.Method: refined / Origin x: 36.0064 Å / Origin y: 32.0627 Å / Origin z: 25.829 Å
111213212223313233
T0.2631 Å2-0.0586 Å2-0.0202 Å2-0.2865 Å20.0247 Å2--0.282 Å2
L1.4207 °2-0.2921 °2-0.3605 °2-1.4745 °20.3136 °2--1.4275 °2
S-0.0539 Å °0.1393 Å °-0.1612 Å °-0.0543 Å °0.003 Å °0.0494 Å °0.1138 Å °0.0289 Å °0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 225
2X-RAY DIFFRACTION1allB1 - 223
3X-RAY DIFFRACTION1allA - B1 - 300
4X-RAY DIFFRACTION1allA1 - 319
5X-RAY DIFFRACTION1allA - B1 - 370
6X-RAY DIFFRACTION1allA1 - 320
7X-RAY DIFFRACTION1allA1 - 321

+
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