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- PDB-4obm: Crystal structure of a putative transcription regulator (EUBSIR_0... -

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Basic information

Entry
Database: PDB / ID: 4obm
TitleCrystal structure of a putative transcription regulator (EUBSIR_01389) from Eubacterium siraeum DSM 15702 at 2.15 A resolution
ComponentsUncharacterized protein
KeywordsTRANSCRIPTION REGULATOR / PF03816 family / LytR_cpsA_psr / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyLCP protein / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta / Cell envelope-related transcriptional attenuator domain-containing protein
Function and homology information
Biological speciesEubacterium siraeum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (EUBSIR_01389) from Eubacterium siraeum DSM 15702 at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5243
Polymers29,0921
Non-polymers4332
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.503, 51.466, 104.712
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 29091.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium siraeum (bacteria) / Strain: DSM 15702 / Gene: EUBSIR_01389, ZP_02422542.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: B0MNI4
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (24-281) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (24-281) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.5
Details: 40.0000% 2-methyl-2,4-pentanediol, 5.0000% polyethylene glycol 8000, 0.1M sodium cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97953,0.9791
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979531
30.97911
ReflectionResolution: 2.15→46.189 Å / Num. obs: 14819 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.011 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.53
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.15-2.230.512.24490148398
2.23-2.320.4432.64761147699
2.32-2.420.3713.14439137198.4
2.42-2.550.28544735149898.6
2.55-2.710.2184.94470145196.9
2.71-2.920.1566.74948149399.1
2.92-3.210.118.94695146898.8
3.21-3.670.07712.14501145596.1
3.67-4.610.05914.94745150097.3
4.610.055154650159394.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.15→46.189 Å / Cor.coef. Fo:Fc: 0.8602 / Cor.coef. Fo:Fc free: 0.8493 / Occupancy max: 1 / Occupancy min: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. PEG FRAGMENTS MODELED ARE PRESENT IN CRYSTALLIZATION CONDITIONS. ALTERNATIVELY, THE CORRESPONDING DENSITY FOR 1PE COULD BE MODELED AS FATTY ACIDS. 5. DUE TO WEAK DENSITIES, THE SIDE-CHAIN IDENTITIES OF N-TERMINAL 24-37 CANNOT BE ASSIGNED DEFINITELY. AS A RESULT, THEIR ASSIGNMENTS ARE TENTATIVE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 737 4.99 %RANDOM
Rwork0.2022 ---
obs0.2044 14779 97.74 %-
Displacement parametersBiso max: 116.96 Å2 / Biso mean: 37.7843 Å2 / Biso min: 12.43 Å2
Baniso -1Baniso -2Baniso -3
1-17.9617 Å20 Å20 Å2
2--3.2166 Å20 Å2
3----21.1783 Å2
Refine analyzeLuzzati coordinate error obs: 0.289 Å
Refinement stepCycle: LAST / Resolution: 2.15→46.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 29 155 2197
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d981SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes290HARMONIC5
X-RAY DIFFRACTIONt_it2086HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion300SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2539SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2086HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2826HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion2.8
LS refinement shellResolution: 2.15→2.32 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2744 146 4.88 %
Rwork0.225 2847 -
all0.2274 2993 -
obs--97.74 %
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)
10.9763-0.44810.68990.0274-0.18090.26330.0041-0.0259-0.00540.02660.0023-0.0020.0362-0.0017-0.00640.01560.0113-0.051-0.01530.02060.024746.038657.55911.7698
21.2855-0.25260.1220.99220.17870.6163-0.01560.20780.0275-0.0872-0.0202-0.0252-0.00750.020.03580.03270.0010.002-0.0282-0.0178-0.185969.293954.582341.2528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|24 - 37}A24 - 37
2X-RAY DIFFRACTION2{A|38 - 281}A38 - 281

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