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- PDB-2o0m: The crystal structure of the putative SorC family transcriptional... -

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Basic information

Entry
Database: PDB / ID: 2o0m
TitleThe crystal structure of the putative SorC family transcriptional regulator from Enterococcus faecalis
ComponentsTranscriptional regulator, SorC familyTranscriptional regulation
KeywordsTRANSCRIPTION / SorC family / transcriptional regulator / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Sugar-binding domain, putative / Putative sugar-binding domain / Rossmann fold - #1360 / NagB/RpiA transferase-like / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Transcriptional regulator, SorC family
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsZhang, R. / Zhou, M. / Bargassa, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the putative SorC family transcriptional regulator from Enterococcus faecalis
Authors: Zhang, R. / Zhou, M. / Bargassa, M. / Joachimiak, A.
History
DepositionNov 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT OF THE PROTEIN IS NOT KNOWN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, SorC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5823
Polymers39,3921
Non-polymers1902
Water6,792377
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.398, 41.660, 64.267
Angle α, β, γ (deg.)90.00, 118.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

21A-466-

HOH

31A-532-

HOH

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Components

#1: Protein Transcriptional regulator, SorC family / Transcriptional regulation


Mass: 39391.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q833I7
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

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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: 1.72 Å3/Da
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Ammonium Sulfate, 0.1M Tris, 25% PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2006 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.6→56.52 Å / Num. all: 33906 / Num. obs: 33635 / % possible obs: 0.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 15.93
Reflection shellResolution: 1.6→1.642 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.46 / Num. unique all: 2468 / % possible all: 93.48

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→56.52 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.546 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.112 / ESU R Free: 0.086
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20089 1777 5 %RANDOM
Rwork0.164 ---
all0.1659 33906 --
obs0.1659 33635 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.952 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0.34 Å2
2--1.48 Å20 Å2
3----2.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.042 Å0.032 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 1.6→56.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 10 377 2289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221937
X-RAY DIFFRACTIONr_bond_other_d0.0010.021795
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9682614
X-RAY DIFFRACTIONr_angle_other_deg0.76234185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3655246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03725.18183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50915358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0391510
X-RAY DIFFRACTIONr_chiral_restr0.0640.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022137
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02356
X-RAY DIFFRACTIONr_nbd_refined0.220.2459
X-RAY DIFFRACTIONr_nbd_other0.1940.21840
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2965
X-RAY DIFFRACTIONr_nbtor_other0.0840.21012
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2278
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3780.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.248
X-RAY DIFFRACTIONr_mcbond_it1.1831.51499
X-RAY DIFFRACTIONr_mcbond_other0.3481.5507
X-RAY DIFFRACTIONr_mcangle_it1.3721965
X-RAY DIFFRACTIONr_scbond_it2.7853795
X-RAY DIFFRACTIONr_scangle_it3.7264.5649
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 130 -
Rwork0.197 2307 -
obs-2307 93.48 %
Refinement TLS params.Method: refined / Origin x: -0.866 Å / Origin y: 26.651 Å / Origin z: 16.703 Å
111213212223313233
T0.0379 Å2-0.0027 Å2-0.0145 Å2-0.013 Å2-0.0028 Å2--0.0628 Å2
L0.2057 °20.0129 °2-0.184 °2-0.1473 °2-0.0121 °2--0.7431 °2
S-0.0142 Å °-0.0161 Å °-0.0061 Å °0.0255 Å °0.0054 Å °-0.0094 Å °-0.0083 Å °0.0877 Å °0.0088 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA95 - 15095 - 150
2X-RAY DIFFRACTION1AA151 - 200151 - 200
3X-RAY DIFFRACTION1AA201 - 250201 - 250
4X-RAY DIFFRACTION1AA251 - 300251 - 300
5X-RAY DIFFRACTION1AA301 - 341301 - 341

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