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- PDB-1z05: Crystal structure of the ROK family transcriptional regulator, ho... -

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Basic information

Entry
Database: PDB / ID: 1z05
TitleCrystal structure of the ROK family transcriptional regulator, homolog of E.coli MLC protein.
Componentstranscriptional regulator, ROK familyTranscriptional regulation
KeywordsTRANSCRIPTION / ROK family / transcriptional regulator / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / metal ion binding
Similarity search - Function
ROK family signature. / ROK family / ROK family / ATPase, nucleotide binding domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...ROK family signature. / ROK family / ROK family / ATPase, nucleotide binding domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Transcriptional regulator, ROK family
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar eltor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMinasov, G. / Brunzelle, J.S. / Shuvalova, L. / Collart, F.R. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of the ROK family transcriptional regulator, homolog of E.coli MLC protein.
Authors: Minasov, G. / Brunzelle, J.S. / Shuvalova, L. / Collart, F.R. / Anderson, W.F.
History
DepositionMar 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jun 27, 2018Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: transcriptional regulator, ROK family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,89710
Polymers47,0851
Non-polymers8129
Water7,134396
1
A: transcriptional regulator, ROK family
hetero molecules

A: transcriptional regulator, ROK family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,79320
Polymers94,1692
Non-polymers1,62418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)93.719, 93.719, 118.291
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsProbably a dimer. The secon part could be generated by the two fold axis: -y,-x,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein transcriptional regulator, ROK family / Transcriptional regulation


Mass: 47084.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar eltor (bacteria)
Species: Vibrio cholerae / Strain: N16961 / Gene: AAF95155 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9KQJ1

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Non-polymers , 5 types, 405 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 3 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, 1.5M Ammonium SO4, 12% Glycerol, 5mM beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 9, 2005 / Details: Mirror
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 33945 / Num. obs: 33945 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 16.5 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 52.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 7.9 / Num. unique all: 3580 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.11 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Individual isotropic b-factor refinement
Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22429 1651 5 %RANDOM
Rwork0.18501 ---
obs0.18702 31297 90.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.342 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å20 Å2
2---1.58 Å20 Å2
3---3.16 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3045 0 41 396 3482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223287
X-RAY DIFFRACTIONr_angle_refined_deg1.0981.9744480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2925426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18424.899149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89715573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0761520
X-RAY DIFFRACTIONr_chiral_restr0.0740.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022490
X-RAY DIFFRACTIONr_nbd_refined0.1830.21582
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22316
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2320
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.222
X-RAY DIFFRACTIONr_mcbond_it1.0481.52132
X-RAY DIFFRACTIONr_mcangle_it1.67123331
X-RAY DIFFRACTIONr_scbond_it2.77631288
X-RAY DIFFRACTIONr_scangle_it4.2364.51149
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 144 -
Rwork0.217 2461 -
obs--99.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.1598-2.05752.12394.7606-2.54395.24510.07380.0499-0.06960.23740.03450.3346-0.1264-0.1312-0.1083-0.2467-0.00890.0213-0.11680.0277-0.1675-7.562224.455616.6833
22.845-0.37581.09434.4043-0.97672.2518-0.06-0.09070.07190.519-0.0586-0.3053-0.14880.12870.1185-0.114-0.0059-0.0586-0.2065-0.0298-0.219817.122120.158234.014
32.3236-1.7145-0.67552.07430.50430.78740.0769-0.00070.0535-0.03070.0727-0.1438-0.04780.1789-0.1495-0.1324-0.016-0.0017-0.1482-0.0618-0.173421.2413-3.388222.6964
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA14 - 8238 - 106
2X-RAY DIFFRACTION1AA395 - 405419 - 429
3X-RAY DIFFRACTION2AA83 - 192107 - 216
4X-RAY DIFFRACTION3AA193 - 394217 - 418

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