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- PDB-1mkm: CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA ICLR -

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Basic information

Entry
Database: PDB / ID: 1mkm
TitleCRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA ICLR
ComponentsIclR transcriptional regulator
KeywordsTRANSCRIPTION / STRUCTURAL GENOMICS / WINGED HELIX-TURN-HELIX / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Single helix bin / helix_turn_helix isocitrate lyase regulation / Bacterial transcriptional regulator / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / IclR helix-turn-helix domain / IclR-type HTH domain profile. / IclR effector binding domain profile. / ArsR-like helix-turn-helix domain / GAF domain ...Single helix bin / helix_turn_helix isocitrate lyase regulation / Bacterial transcriptional regulator / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / IclR helix-turn-helix domain / IclR-type HTH domain profile. / IclR effector binding domain profile. / ArsR-like helix-turn-helix domain / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Transcriptional regulator, IclR family
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsKim, Y. / Zhang, R.G. / Joachimiak, A. / Skarina, T. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family.
Authors: Zhang, R.G. / Kim, Y. / Skarina, T. / Beasley, S. / Laskowski, R. / Arrowsmith, C. / Edwards, A. / Joachimiak, A. / Savchenko, A.
History
DepositionAug 29, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionSep 11, 2002ID: 1JMR
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IclR transcriptional regulator
B: IclR transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0695
Polymers56,8922
Non-polymers1773
Water2,000111
1
A: IclR transcriptional regulator
B: IclR transcriptional regulator
hetero molecules

A: IclR transcriptional regulator
B: IclR transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,13810
Polymers113,7844
Non-polymers3546
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)115.229, 61.076, 95.911
Angle α, β, γ (deg.)90.00, 110.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein IclR transcriptional regulator


Mass: 28446.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WXS0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000, Glycerol, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MHEPES1reservoirpH7.
25 %PEG80001reservoir
35 %glycerol1reservoir
49 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97946, 0.97955, 0.93927
DetectorType: SBC-2 / Detector: CCD / Date: Feb 10, 2001
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR, SAGITALLY FOCUSED SI-111, SI-220
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979461
20.979551
30.939271
ReflectionResolution: 2.2→50 Å / Num. all: 27598 / Num. obs: 27598 / % possible obs: 85.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 15.9
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 2.5 / % possible all: 59.6
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / Redundancy: 3 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 2.2 Å / % possible obs: 59.6 % / Mean I/σ(I) obs: 2.5

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Processing

Software
NameClassification
d*TREKdata scaling
SCALEPACKdata scaling
CNSrefinement
d*TREKdata reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→31.24 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.3 2225 10 %RANDOM
Rwork0.232 ---
all0.257 22290 --
obs0.257 22290 69.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.57 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 65.5 Å2
Baniso -1Baniso -2Baniso -3
1-28.09 Å20 Å220.11 Å2
2---16.63 Å20 Å2
3----11.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.2→31.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3968 0 2 114 4084
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.281.5
X-RAY DIFFRACTIONc_mcangle_it7.032
X-RAY DIFFRACTIONc_scbond_it7.472
X-RAY DIFFRACTIONc_scangle_it9.492.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 215 10.7 %
Rwork0.313 1798 -
obs-2013 37.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor Rfree: 0.3
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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