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- PDB-2g7g: The Crystal Structure of the Putative Transcriptional Regulator R... -

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Basic information

Entry
Database: PDB / ID: 2g7g
TitleThe Crystal Structure of the Putative Transcriptional Regulator Rha04620 from Rhodococcus sp. RHA1
ComponentsRha04620, Putative Transcriptional Regulator
KeywordsTRANSCRIPTION / helix-turn-helix / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


response to antibiotic / negative regulation of DNA-templated transcription
Similarity search - Function
Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, C-terminal domain / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETIC ACID / Probable tetracycline repressor
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsKim, Y. / Joachimiak, A. / Evdokimova, E. / Kagan, O. / Savchenko, A. / Edwards, A.M. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of the Putative Transcriptional Regulator Rha04620 from Rhodococcus sp. RHA1
Authors: Kim, Y. / Joachimiak, A. / Evdokimova, E. / Kagan, O. / Savchenko, A. / Edwards, A.M.
History
DepositionFeb 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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 999SEQUENCE NO SUITABLE SEQUENCE DATABASE WAS AVAILABLE AT THE TIME OF PROCESSING THIS FILE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rha04620, Putative Transcriptional Regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4753
Polymers23,3551
Non-polymers1202
Water2,270126
1
A: Rha04620, Putative Transcriptional Regulator
hetero molecules

A: Rha04620, Putative Transcriptional Regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9506
Polymers46,7092
Non-polymers2404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5270 Å2
ΔGint-45 kcal/mol
Surface area17830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)99.508, 99.508, 40.472
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-334-

HOH

Detailsdimer, the other monomer is generated by applying the operator: y, x, -z

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Components

#1: Protein Rha04620, Putative Transcriptional Regulator


Mass: 23354.697 Da / Num. of mol.: 1 / Fragment: Rha04620
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: RHA1 / Gene: rha04620 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q0S9X7
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 3.9 M Ammonium Acetate, 0.1M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2006 / Details: mirrors
RadiationMonochromator: double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2→44.5 Å / Num. all: 14221 / Num. obs: 13817 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.7 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 3.44 / Num. unique all: 1088 / % possible all: 79.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
MLPHAREphasing
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→44.5 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.48 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.192
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.24469 1375 10 %RANDOM
Rwork0.19074 ---
all0.19607 12402 --
obs0.19607 12402 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.132 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å20 Å2
2--1.44 Å20 Å2
3----2.88 Å2
Refinement stepCycle: LAST / Resolution: 2.01→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 8 126 1644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211658
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.9392263
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0135216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23121.97786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.09215254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.441522
X-RAY DIFFRACTIONr_chiral_restr0.0910.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021342
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.2750
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21150
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2113
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9631.51079
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59221665
X-RAY DIFFRACTIONr_scbond_it2.5933643
X-RAY DIFFRACTIONr_scangle_it4.0214.5598
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 89 -
Rwork0.211 668 -
obs-668 75.4 %
Refinement TLS params.Method: refined / Origin x: 25.084 Å / Origin y: 28.6835 Å / Origin z: 8.347 Å
111213212223313233
T-0.0736 Å20.0425 Å2-0.0164 Å2--0.0445 Å20.0471 Å2---0.1083 Å2
L0.0879 °20.1528 °20.0318 °2-0.3439 °20.2255 °2--0.4936 °2
S0.0255 Å °-0.0516 Å °-0.0564 Å °0.0109 Å °-0.0119 Å °-0.0507 Å °-0.0228 Å °0.0038 Å °-0.0136 Å °

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