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- PDB-3efb: Crystal Structure of Probable sor Operon Regulator from Shigella ... -

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Basic information

Entry
Database: PDB / ID: 3efb
TitleCrystal Structure of Probable sor Operon Regulator from Shigella flexneri
ComponentsProbable sor-operon regulator
KeywordsTRANSCRIPTION / alpha-beta-alpha sandwich / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Transposase IS30-like HTH domain / Helix-turn-helix domain / Sugar-binding domain, putative / Putative sugar-binding domain / Rossmann fold - #1360 / ArsR-like helix-turn-helix domain / NagB/RpiA transferase-like / Homeobox-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Probable sor-operon regulator / Probable sor-operon regulator
Similarity search - Component
Biological speciesShigella flexneri 2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.001 Å
AuthorsKim, Y. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Probable sor Operon Regulator from Shigella flexneri
Authors: Kim, Y. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A. / Anderson, W.F. / Joachimiak, A.
History
DepositionSep 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable sor-operon regulator
B: Probable sor-operon regulator
C: Probable sor-operon regulator
D: Probable sor-operon regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,0855
Polymers118,0254
Non-polymers601
Water8,989499
1
A: Probable sor-operon regulator
D: Probable sor-operon regulator


Theoretical massNumber of molelcules
Total (without water)59,0132
Polymers59,0132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-10 kcal/mol
Surface area20450 Å2
MethodPISA
2
B: Probable sor-operon regulator
C: Probable sor-operon regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0733
Polymers59,0132
Non-polymers601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-11 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.536, 238.463, 53.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Probable sor-operon regulator


Mass: 29506.320 Da / Num. of mol.: 4 / Fragment: UNP residues 51-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a (bacteria) / Strain: 2457T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q83PA8, UniProt: A0A0H2V3A6*PLUS
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE TARGET ID IDP01531 DOES NOT EXIST IN TARGETDB AT THE TIME OF PROCESSING.

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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: 1.89 Å3/Da / Density % sol: 34.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M calsium acetate, 9% PEG 8000, 0.1M sodium cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793, 0.9795
DetectorType: SBC-3 / Detector: CCD / Date: Feb 18, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
ReflectionResolution: 2→33.38 Å / Num. all: 61178 / Num. obs: 61178 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 36.8 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 6.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2 / Num. unique obs: 1528 / % possible all: 49.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
Cootmodel building
PHENIX(phenix.refine)/refmac5.5refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.001→33.378 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): 0 / Stereochemistry target values: MLHL / Details: Refmac 5.5 was also used for refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3090 5.06 %random
Rwork0.2 ---
all0.203 61074 --
obs0.203 61074 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.801 Å2 / ksol: 0.337 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.3522 Å2-0 Å20 Å2
2---3.8133 Å2-0 Å2
3---13.1655 Å2
Refinement stepCycle: LAST / Resolution: 2.001→33.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7409 0 4 499 7912
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_deg1.164
X-RAY DIFFRACTIONf_dihedral_angle_d18.37
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0011-2.03230.32321310.25772401X-RAY DIFFRACTION93
2.0323-2.06560.30731460.23832584X-RAY DIFFRACTION99
2.0656-2.10130.27871480.23782608X-RAY DIFFRACTION100
2.1013-2.13950.31991420.22852575X-RAY DIFFRACTION100
2.1395-2.18060.29521390.22862604X-RAY DIFFRACTION100
2.1806-2.22510.28421260.22072631X-RAY DIFFRACTION100
2.2251-2.27350.29541240.2162613X-RAY DIFFRACTION100
2.2735-2.32630.26581390.21152667X-RAY DIFFRACTION100
2.3263-2.38450.26591370.19342592X-RAY DIFFRACTION100
2.3845-2.4490.25071420.20052655X-RAY DIFFRACTION100
2.449-2.5210.25191390.19162599X-RAY DIFFRACTION100
2.521-2.60230.26471410.19832630X-RAY DIFFRACTION100
2.6023-2.69530.27961360.20312666X-RAY DIFFRACTION100
2.6953-2.80320.26211330.20952625X-RAY DIFFRACTION100
2.8032-2.93070.28281500.22752660X-RAY DIFFRACTION100
2.9307-3.08510.29281410.222629X-RAY DIFFRACTION100
3.0851-3.27820.26561540.21542648X-RAY DIFFRACTION100
3.2782-3.53110.22371240.18082702X-RAY DIFFRACTION100
3.5311-3.88590.17481420.15822683X-RAY DIFFRACTION100
3.8859-4.44710.17961590.14682689X-RAY DIFFRACTION100
4.4471-5.59860.2241420.16272726X-RAY DIFFRACTION100
5.5986-33.38250.27141550.21472797X-RAY DIFFRACTION97
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)
10.83870.11630.03882.6509-0.19431.4079-0.0638-0.01410.0449-0.1243-0.04550.64470.0286-0.07150.12410.25420.0071-0.03440.1052-0.05540.2518-21.400215.759214.5412
21.53340.08310.14582.1254-0.2840.4847-0.010.10780.0496-0.30640.02410.1622-0.06850.0799-0.01680.37190.0067-0.04420.13840.05550.088830.315145.631330.9488
30.70360.3465-0.15122.8145-0.2961.1909-0.1043-0.04660.0876-0.04330.15940.62980.119-0.0304-0.03570.28080.01580.01160.15710.05540.255916.132715.231141.241
41.02520.7521-0.11432.3457-0.09590.88070.00580.11190.1363-0.5802-0.0460.3675-0.05080.11030.03570.53560.0214-0.130.14290.05050.171-4.24144.83262.9805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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