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- PDB-3mz1: The crystal structure of a possible TRANSCRIPTION REGULATOR PROTE... -

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Basic information

Entry
Database: PDB / ID: 3mz1
TitleThe crystal structure of a possible TRANSCRIPTION REGULATOR PROTEIN from Sinorhizobium meliloti 1021
ComponentsPutative transcriptional regulator
Keywordstranscription regulator / structural genomics / PSI-2 / protein structure initiative / midwest center for str uctural genomics / MCSG / Midwest Center for Structural Genomics
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative transcriptional regulator
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å
AuthorsTan, K. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a possible TRANSCRIPTION REGULATOR PROTEIN from Sinorhizobium meliloti 1021
Authors: Tan, K. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionMay 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative transcriptional regulator
B: Putative transcriptional regulator
C: Putative transcriptional regulator
D: Putative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,1985
Polymers136,1624
Non-polymers351
Water6,539363
1
A: Putative transcriptional regulator
B: Putative transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)68,0812
Polymers68,0812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-11 kcal/mol
Surface area19500 Å2
MethodPISA
2
C: Putative transcriptional regulator
D: Putative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1173
Polymers68,0812
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-19 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.345, 83.325, 85.067
Angle α, β, γ (deg.)90.00, 91.65, 90.00
Int Tables number4
Space group name H-MP1211
DetailsExperimentally unknown. THe chains A and B, C and D like form dimers, respectively.

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Components

#1: Protein
Putative transcriptional regulator


Mass: 34040.570 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: R00429, SMc01092 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q92SG7
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 1.76 Å3/Da / Density % sol: 29.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES, 0.2M Ammonium sulfate, 30% PEG5Kmme, 1/10V8, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.88→37 Å / Num. all: 75983 / Num. obs: 75983 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 23.1
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3780 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.88→36.422 Å / SU ML: 0.24 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 3600 5.02 %random
Rwork0.1845 ---
all0.1865 71737 --
obs0.1865 71737 93.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.51 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.4719 Å2-0 Å23.7436 Å2
2---4.1241 Å2-0 Å2
3---8.596 Å2
Refinement stepCycle: LAST / Resolution: 1.88→36.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6653 0 1 363 7017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076912
X-RAY DIFFRACTIONf_angle_d1.1669407
X-RAY DIFFRACTIONf_dihedral_angle_d16.6742599
X-RAY DIFFRACTIONf_chiral_restr0.0791042
X-RAY DIFFRACTIONf_plane_restr0.0061233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8801-1.94730.28952890.24585598X-RAY DIFFRACTION77
1.9473-2.02530.27743220.20916308X-RAY DIFFRACTION87
2.0253-2.11740.23413550.19246579X-RAY DIFFRACTION91
2.1174-2.22910.2373830.18896752X-RAY DIFFRACTION94
2.2291-2.36870.23823340.17476993X-RAY DIFFRACTION96
2.3687-2.55150.23643640.1887044X-RAY DIFFRACTION97
2.5515-2.80820.25023770.19587112X-RAY DIFFRACTION98
2.8082-3.21440.22063960.18687194X-RAY DIFFRACTION99
3.2144-4.04890.20794040.16657221X-RAY DIFFRACTION100
4.0489-36.42910.19523760.17657336X-RAY DIFFRACTION99
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)
13.07980.36330.7831.3-0.84260.8975-0.084-0.10490.1760.00080.05280.0697-0.0151-0.1032-0.02470.1162-0.0003-0.02670.1043-0.01140.1416-35.368419.6966-37.7916
22.4106-1.05451.29712.1055-0.30411.7309-0.15880.04780.5884-0.0525-0.0626-0.0974-0.24240.06130.12460.1518-0.0202-0.01930.11070.03520.2529-14.699737.127-42.4701
33.5512-0.4543-0.3110.611-0.46681.1294-0.0793-0.0933-0.04740.04780.0078-0.0924-0.01340.12070.0390.1260.03380.00560.2080.00570.1470.992919.0412-35.6974
42.38310.1920.26121.8023-0.65392.0257-0.0295-0.26160.06220.1614-0.03130.062-0.05560.0254-0.00280.1052-0.00110.01570.13010.02420.0591-19.699913.2059-19.2119
53.76230.3667-1.16671.0254-0.391.8732-0.2584-0.4505-0.6152-0.0353-0.067-0.26260.07010.34260.30330.18230.06910.06890.25060.06020.345633.490419.02296.5161
62.3034-0.12420.361.6857-0.05492.1987-0.0389-0.2695-0.08860.064-0.1337-0.17660.0857-0.00410.16520.1646-0.0044-0.00520.20340.06850.16711.87311.480622.1592
72.99160.14180.72381.8516-0.76850.6053-0.1355-0.14240.2276-0.01380.03220.007-0.0482-0.09090.04580.1618-0.0041-0.02990.1163-0.04360.1325-2.926620.07315.1106
82.0746-0.7882-0.01862.6610.70680.9193-0.0212-0.01330.1165-0.16540.02690.0264-0.11120.0111-0.00220.1427-0.01270.01780.110.01030.131917.294937.66631.9096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 155:262
2X-RAY DIFFRACTION2chain A not resid 155:262
3X-RAY DIFFRACTION3chain B and resid 155:262
4X-RAY DIFFRACTION4chain B not resid 155:262
5X-RAY DIFFRACTION5chain C and resid 155:262
6X-RAY DIFFRACTION6chain C not resid 155:262
7X-RAY DIFFRACTION7chain D and resid 155:262
8X-RAY DIFFRACTION8chain D not resid 155:262

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