[English] 日本語
Yorodumi
- PDB-3mlf: Putative transcriptional regulator from Staphylococcus aureus. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mlf
TitlePutative transcriptional regulator from Staphylococcus aureus.
Componentstranscriptional regulatorTranscriptional regulation
Keywordstranscription regulator / structural genomics / Helix-turn-helix XRE-family like protein / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologylambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsOsipiuk, J. / Tesar, C. / Gornicki, P. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of putative transcriptional regulator from Staphylococcus aureus.
Authors: Osipiuk, J. / Tesar, C. / Gornicki, P. / Joachimiak, A.
History
DepositionApr 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 8, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: transcriptional regulator
B: transcriptional regulator
C: transcriptional regulator
D: transcriptional regulator
E: transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)65,6065
Polymers65,6065
Non-polymers00
Water2,306128
1
A: transcriptional regulator
B: transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)26,2422
Polymers26,2422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-18 kcal/mol
Surface area10830 Å2
MethodPISA
2
C: transcriptional regulator
D: transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)26,2422
Polymers26,2422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-17 kcal/mol
Surface area10590 Å2
MethodPISA
3
E: transcriptional regulator

E: transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)26,2422
Polymers26,2422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+3/21
Buried area2030 Å2
ΔGint-16 kcal/mol
Surface area10320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.776, 159.776, 69.344
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Detailsputative biological unit is a dimer

-
Components

#1: Protein
transcriptional regulator / Transcriptional regulation


Mass: 13121.135 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: USA300_TCH1516 / Gene: USA300HOU_2003 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8Z4R3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 3.37 Å3/Da / Density % sol: 63.53 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M TRIS buffer, 1.4 M di-ammonium tartrate, 1 mM magnesium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→44.3 Å / Num. all: 27459 / Num. obs: 27459 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 59.3 Å2 / Rmerge(I) obs: 0.146 / Χ2: 3.038 / Net I/σ(I): 8.3
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1386 / Χ2: 1.161 / % possible all: 99.4

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→44.3 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 20.812 / SU ML: 0.195 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.349 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1376 5 %RANDOM
Rwork0.208 ---
all0.21 27422 --
obs0.21 27422 97.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.1 Å2 / Biso mean: 24.902 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3774 0 0 128 3902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223920
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.9685252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.825479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54125.9200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.13715823
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3521512
X-RAY DIFFRACTIONr_chiral_restr0.1130.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022874
X-RAY DIFFRACTIONr_mcbond_it0.7371.52309
X-RAY DIFFRACTIONr_mcangle_it1.47523737
X-RAY DIFFRACTIONr_scbond_it2.61431611
X-RAY DIFFRACTIONr_scangle_it4.3334.51502
LS refinement shellResolution: 2.601→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 110 -
Rwork0.311 1864 -
all-1974 -
obs-1974 97.19 %
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)
12.1614-3.2109-0.29615.48642.74927.51840.16450.15960.1958-0.3673-0.1916-0.2962-0.46560.11340.0270.12210.06380.0110.17050.0280.139822.38941.782231.6565
20.88881.36941.00735.0739-0.79713.02260.1370.1523-0.1678-0.0433-0.0397-0.37130.26550.3955-0.09730.17270.0358-0.01850.09990.00140.122817.880856.912321.5078
30.1156-0.3697-0.58917.0591-0.03883.65590.04150.093-0.0189-0.0414-0.01790.3561-0.0997-0.57-0.02360.1672-0.00210.01260.09830.01630.1347.54336.024457.3224
43.9139-2.32971.10771.5021-1.33044.34480.15490.2316-0.318-0.1698-0.08590.19540.5945-0.242-0.0690.16010.0159-0.0110.1636-0.03710.10310.543250.143967.9287
50.68171.44680.53854.3083-0.56283.14880.0447-0.10440.09120.1119-0.0220.2504-0.0927-0.2547-0.02260.1094-0.0107-0.02740.0774-0.00950.11122.14019.93155.1258
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-9 - 85
2X-RAY DIFFRACTION1A88 - 127
3X-RAY DIFFRACTION2B-7 - 84
4X-RAY DIFFRACTION2B88 - 112
5X-RAY DIFFRACTION3C-7 - 84
6X-RAY DIFFRACTION3C88 - 126
7X-RAY DIFFRACTION4D-7 - 85
8X-RAY DIFFRACTION4D88 - 125
9X-RAY DIFFRACTION5E0 - 85
10X-RAY DIFFRACTION5E88 - 128

+
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