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- PDB-4lzl: Structure of the inactive form of the regulatory domain from the ... -

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Basic information

Entry
Database: PDB / ID: 4lzl
TitleStructure of the inactive form of the regulatory domain from the repressor of iron transport regulator (RitR)
ComponentsResponse regulator
KeywordsTRANSCRIPTION / Two-component response regulator
Function / homologyResponse regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesStreptococcus pneumoniae 2061617 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSilvaggi, N.R. / Han, L. / Ulijasz, A.T.
CitationJournal: To be Published
Title: Defining the Aspartate-Less Receiver (ALR) Domains: Structure and Activation of RitR from Streptococcus pneumoniae
Authors: Maule, A.F. / Weiner, J.J. / Han, L. / Wright, D.P. / Peterson, F.C. / Volkman, B.F. / Silvaggi, N.R. / Ulijasz, A.T.
History
DepositionJul 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5632
Polymers14,4711
Non-polymers921
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.460, 33.840, 34.960
Angle α, β, γ (deg.)92.65, 103.71, 97.53
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Response regulator


Mass: 14470.814 Da / Num. of mol.: 1 / Fragment: N-terminal Regulatory Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae 2061617 (bacteria)
Strain: G54 / Gene: AMCSP02_000425, RitR / Plasmid: pE-SUMOkan / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: J1QDX6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1ul 5-10 mg/ml protein in 10.0 mM BIS-TRIS propane, pH 7.5 plus 1ul of 20-25% polyethylene glycol (PEG) 3350, 2.5 mM magnesium formate, and 20.0 mM TRIS, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97931 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.55→33.85 Å / Num. all: 18275 / Num. obs: 17289 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 12.5
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 3 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 7.3 / Num. unique all: 2488 / % possible all: 93

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Processing

Software
NameVersionClassification
MD2data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MVO

1mvo


Resolution: 1.55→27.352 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 2.37 / Phase error: 14.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1614 1739 10.06 %RANDOM
Rwork0.1411 ---
obs0.1431 17288 94.62 %-
all-18271 --
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→27.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1007 0 6 189 1202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091137
X-RAY DIFFRACTIONf_angle_d1.2041545
X-RAY DIFFRACTIONf_dihedral_angle_d12.714446
X-RAY DIFFRACTIONf_chiral_restr0.078172
X-RAY DIFFRACTIONf_plane_restr0.005202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.548-1.60340.15511700.1451551X-RAY DIFFRACTION93
1.6034-1.66760.18881730.14221545X-RAY DIFFRACTION93
1.6676-1.74340.17851780.15151505X-RAY DIFFRACTION94
1.7434-1.83530.17361640.14861558X-RAY DIFFRACTION94
1.8353-1.95030.17271790.13811546X-RAY DIFFRACTION95
1.9503-2.10080.15731710.14081567X-RAY DIFFRACTION95
2.1008-2.31210.16281700.13581575X-RAY DIFFRACTION95
2.3121-2.64650.1631790.14221583X-RAY DIFFRACTION96
2.6465-3.33330.16581760.14041577X-RAY DIFFRACTION97
3.3333-27.35580.14491790.13971542X-RAY DIFFRACTION94
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)
12.711-1.0447-0.64031.29980.33991.54450.03540.03940.1326-0.0052-0.0453-0.1479-0.07120.02780.00620.0271-0.0022-0.01760.04690.0090.043427.91532.36995.6513
23.8473-1.93740.38147.8825-1.86672.97630.0796-0.24390.33830.0414-0.1294-0.1980.05940.07830.07320.0323-0.0166-0.00930.1288-0.0170.101324.494333.557911.9568
34.1979-1.9149-0.8655.22980.79775.6853-0.0739-0.3780.05290.2470.0954-0.31130.07950.40910.01750.0810.0036-0.01430.13420.02150.043219.39124.918719.5532
42.02340.14960.96043.47990.9723.5063-0.2687-0.22520.29810.46130.02430.3369-0.02620.1089-0.08570.06780.00270.01140.03990.0335-0.042416.207530.933811.833
50.8391-0.1575-1.7242.139-0.3113.8754-0.2309-0.3929-0.17340.48230.1729-0.15280.70310.50360.0970.14870.0649-0.0110.05470.04920.066320.484816.97978.1238
63.65230.2151-2.80471.2-0.09282.1783-0.2555-0.2469-0.45360.22460.110.09230.5044-0.24870.00160.12570.00040.03490.10410.07190.048711.204318.606514.754
71.2815-0.0337-0.57560.883-0.01083.0389-0.1169-0.03350.0397-0.08190.1384-0.01680.24220.06260.01970.0567-0.0227-0.00730.04520.02250.03115.06523.6282.4278
82.1394-0.6418-2.47843.37140.58647.2618-0.30340.1273-0.4106-0.0656-0.21560.35780.6422-0.2110.12010.0912-0.0270.00980.06380.00370.08449.455117.87380.4873
91.14760.3064-0.99620.1607-0.17841.5401-0.010.04950.1359-0.12230.00930.0503-0.0940.1194-0.03320.0729-0.0169-0.00290.05940.01940.026917.382627.5811-2.9507
105.8299-2.25220.63624.1170.0371.5758-0.10380.3514-0.07750.06710.13770.5545-0.0705-0.1494-0.08450.1398-0.00740.01530.04980.02490.152114.768337.7752-0.5346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 5:24 )A5 - 24
2X-RAY DIFFRACTION2( CHAIN A AND RESID 25:34 )A25 - 34
3X-RAY DIFFRACTION3( CHAIN A AND RESID 35:45 )A35 - 45
4X-RAY DIFFRACTION4( CHAIN A AND RESID 46:52 )A46 - 52
5X-RAY DIFFRACTION5( CHAIN A AND RESID 53:60 )A53 - 60
6X-RAY DIFFRACTION6( CHAIN A AND RESID 61:70 )A61 - 70
7X-RAY DIFFRACTION7( CHAIN A AND RESID 71:86 )A71 - 86
8X-RAY DIFFRACTION8( CHAIN A AND RESID 87:96 )A87 - 96
9X-RAY DIFFRACTION9( CHAIN A AND RESID 97:106 )A97 - 106
10X-RAY DIFFRACTION10( CHAIN A AND RESID 107:124 )A107 - 124

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