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- PDB-4aih: Crystal structure of RovA from Yersinia in its free form -

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Basic information

Entry
Database: PDB / ID: 4aih
TitleCrystal structure of RovA from Yersinia in its free form
ComponentsTRANSCRIPTIONAL REGULATOR SLYA
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR / GLOBAL REGULATOR / VIRULENCE REGULATION / THERMOSENSING
Function / homology
Function and homology information


DNA-binding transcription activator activity / DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / positive regulation of DNA-templated transcription
Similarity search - Function
Transcriptional regulator, SlyA / Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / : / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...Transcriptional regulator, SlyA / Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / : / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator SlyA
Similarity search - Component
Biological speciesYERSINIA PSEUDOTUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsQuade, N. / Mendonca, C. / Herbst, K. / Heroven, A.K. / Heinz, D.W. / Dersch, P.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Basis for Intrinsic Thermosensing by the Master Virulence Regulator Rova of Yersinia.
Authors: Quade, N. / Mendonca, C. / Herbst, K. / Heroven, A.K. / Ritter, C. / Heinz, D.W. / Dersch, P.
History
DepositionFeb 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSCRIPTIONAL REGULATOR SLYA
B: TRANSCRIPTIONAL REGULATOR SLYA
C: TRANSCRIPTIONAL REGULATOR SLYA
D: TRANSCRIPTIONAL REGULATOR SLYA
E: TRANSCRIPTIONAL REGULATOR SLYA
F: TRANSCRIPTIONAL REGULATOR SLYA


Theoretical massNumber of molelcules
Total (without water)103,3916
Polymers103,3916
Non-polymers00
Water1,78399
1
A: TRANSCRIPTIONAL REGULATOR SLYA
B: TRANSCRIPTIONAL REGULATOR SLYA


Theoretical massNumber of molelcules
Total (without water)34,4642
Polymers34,4642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-36.6 kcal/mol
Surface area15350 Å2
MethodPISA
2
C: TRANSCRIPTIONAL REGULATOR SLYA
D: TRANSCRIPTIONAL REGULATOR SLYA


Theoretical massNumber of molelcules
Total (without water)34,4642
Polymers34,4642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-33.5 kcal/mol
Surface area15080 Å2
MethodPISA
3
E: TRANSCRIPTIONAL REGULATOR SLYA
F: TRANSCRIPTIONAL REGULATOR SLYA


Theoretical massNumber of molelcules
Total (without water)34,4642
Polymers34,4642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-35.1 kcal/mol
Surface area14400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.160, 74.780, 181.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.54547, 0.14646, 0.82524), (0.18697, -0.98106, 0.05052), (0.81701, 0.12674, -0.56252)4.61371, 29.22113, -14.48427
2given(0.60592, -0.05676, 0.7935), (0.67358, 0.56729, -0.47377), (-0.42325, 0.82156, 0.38197)9.24712, -29.38224, -10.12216
3given(0.10669, 0.66164, 0.74219), (-0.64947, -0.51883, 0.55589), (0.75287, -0.54134, 0.37436)0.32769, 55.47554, -3.94481
4given(0.33108, -0.38757, -0.86033), (-0.33535, -0.90056, 0.27664), (-0.882, 0.19692, -0.42813)-7.43053, 0.85526, -29.75674
5given(-0.55672, -0.09309, -0.82547), (0.32021, 0.89286, -0.31665), (0.7665, -0.44061, -0.46727)-22.54861, 21.34627, -2.50879

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Components

#1: Protein
TRANSCRIPTIONAL REGULATOR SLYA / REGULATOR OF VIRULENCE PROTEIN A / TRANSCRIPTIONAL REGULATOR FOR CRYPTIC HEMOLYSIN / ROVA


Mass: 17231.768 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PSEUDOTUBERCULOSIS (bacteria) / Strain: YPIII / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: B1JJ73
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 108 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 108 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 108 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 108 TO SER ENGINEERED RESIDUE IN CHAIN D, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN D, CYS 108 TO SER ENGINEERED RESIDUE IN CHAIN E, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN E, CYS 108 TO SER ENGINEERED RESIDUE IN CHAIN F, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN F, CYS 108 TO SER

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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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M MES PH 6.5, 20% PEG2000MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.4→90 Å / Num. obs: 36510 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 16.8
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DEU
Resolution: 2.4→90.57 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.933 / SU B: 20.138 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.44 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26612 1824 5 %RANDOM
Rwork0.22024 ---
obs0.22262 34623 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.224 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--1.17 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 2.4→90.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6205 0 0 99 6304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196268
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.9938472
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9065772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.7924.672259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.113151257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6731552
X-RAY DIFFRACTIONr_chiral_restr0.0850.21050
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214424
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.22859
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.24344
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2162
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 109 -
Rwork0.252 2314 -
obs--99.96 %
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)
13.2955-1.43980.470610.52-4.05276.3777-0.1492-0.49580.27990.3140.40920.4471-0.5838-0.3355-0.260.1365-0.00150.03850.2613-0.00590.1853-32.473214.636-20.9998
24.7439-1.14260.52663.895-0.43794.0069-0.0717-0.1044-0.14680.13410.1117-0.14750.26130.185-0.040.14940.0069-0.02030.1793-0.00310.11-16.1336-0.7521-18.7839
316.2955-0.74622.77027.24468.72111.3294-0.09290.58841.0631-0.32320.0477-0.1462-0.39130.22940.04520.35920.10850.14820.2466-0.0530.2403-4.0874-8.6911-27.0447
412.3094-5.94482.02157.3155-1.70533.3424-0.1272-0.4306-1.12350.03220.40460.73710.4675-0.3246-0.27740.252-0.1027-0.02580.13910.08120.1722-25.1623-8.0474-16.5253
515.40936.1493-3.04959.0463-3.59535.6746-0.04430.4137-0.1624-0.5174-0.03410.12570.1572-0.06520.07840.27680.1232-0.05760.3269-0.06720.2007-33.10029.8024-33.983
65.27633.2622-0.760212.1578-0.93393.10320.12950.1053-0.3263-0.0974-0.1057-0.0728-0.02860.2009-0.02380.1820.08140.02180.32320.02140.1843-24.332913.1518-28.65
73.8855-1.1584-2.57852.2081.0499.11030.0389-0.1824-0.1478-0.00850.0874-0.16160.37120.1353-0.12630.1878-0.03580.01150.1720.05090.2026-23.813526.4435-13.5722
83.64420.65721.22693.9690.57148.23040.0385-0.38210.32450.36760.2059-0.4258-0.45350.6718-0.24440.1387-0.0230.02390.2794-0.01430.1786-17.330831.9881-11.6326
92.65490.73060.80191.9761-0.20280.84120.0049-0.04250.0749-0.046-0.07140.4705-0.08260.00490.06650.17150.05790.03430.3017-0.02740.2211-35.339619.2584-28.0743
1059.7687-34.093258.222119.4563-33.207156.7234-4.8594-5.93562.53922.37162.9057-1.4503-4.2702-5.70741.95371.4178-0.1781-0.17611.3195-0.17880.1232-38.47845.684-8.9167
114.03770.3085-0.66993.3715-4.647.66270.0507-0.63980.2110.3835-0.05980.0992-0.8242-0.46350.00910.19630.08230.03560.3834-0.12560.14764.084516.8541-46.0189
127.6995-10.3349-9.203716.075313.421811.5195-0.5673-0.3561-1.5841.4617-0.64140.84560.9804-0.0861.20860.3924-0.369-0.30510.52690.67831.097310.0289-0.3962-37.8124
139.63532.23242.752217.67335.555713.1347-0.36580.4807-0.51450.27020.3116-0.71370.096-0.14540.05420.0955-0.1706-0.03980.35760.06110.095315.35639.6814-36.4575
142.9922-0.779-0.10631.2772-0.82926.75640.1932-0.6581-0.3607-0.01150.05190.15270.3383-0.9004-0.24510.1636-0.15120.11410.33920.05810.24471.30467.4112-44.3571
1541.15315.158715.759816.2802-2.2047.15290.98551.7527-2.71081.5774-0.0992-1.0490.00180.7543-0.88640.44520.2782-0.22430.52-0.35840.387823.05073.8128-58.4977
1613.36890.23481.2684.3361-0.03723.64990.2109-0.7216-0.1920.7072-0.14870.1030.2933-0.1223-0.06210.3960.05120.07540.11940.01280.189212.29079.8945-53.4301
173.81150.8304-0.60113.33310.96034.740.04740.0192-0.07220.229-0.0122-0.2444-0.11860.2207-0.03520.16810.0314-0.02560.22380.06520.103924.396627.6556-48.0984
182.8422.6562.67645.81833.07127.1909-0.1130.23720.19110.3688-0.1019-0.0526-0.38790.91550.21490.1871-0.01140.0420.32150.12940.144530.150329.8024-54.3855
199.2859-0.4829-2.59572.47510.45092.7715-0.00520.79680.2739-0.4179-0.01660.03970.23590.01320.02190.20630.03950.03430.15290.03820.13658.627413.5798-65.8048
2026.373617.6466-20.31333.8532-30.612928.7897-0.78411.7783-0.65810.44441.81571.6318-0.1392-1.8392-1.03170.13810.05030.14580.2576-0.06220.6259-7.083923.3502-54.6315
212.38371.4516-2.36323.3734-2.64055.43530.0610.2962-0.07640.20130.13580.3568-0.0552-0.8045-0.19680.17930.05120.00040.31980.02980.0833-19.34796.708610.8161
224.8463-0.14332.71863.82540.51254.77030.1060.0039-0.2392-0.0549-0.0709-0.14240.21760.0383-0.03510.17870.03390.00430.22840.00010.0476-6.88274.363-0.9775
2319.256-5.0992.49639.9926-3.05680.990.32162.0665-0.09-0.9764-0.6222-1.26080.2720.2880.30060.2970.01170.09430.4208-0.03540.2038-0.92028.8741-6.1133
244.41160.8661-8.7933.2834-4.89529.80940.6142-0.14450.41470.71310.25440.0646-1.7853-0.1695-0.86860.33420.08980.01890.18630.00080.0881-14.906118.06717.7178
2510.7707-11.6892-6.468322.386210.90038.65670.54740.3317-0.3811-0.4269-0.3038-0.87450.21870.6034-0.24360.150.0452-0.04840.38350.02030.1899-9.21863.1327.0145
2611.3385-0.3186-2.435626.93210.204510.2151-0.40180.3781-0.7806-0.7610.6867-0.43020.42391.0248-0.28490.28640.14420.0670.44330.03050.1331-10.317-3.137417.3144
276.88562.07981.14771.03190.51045.2320.16510.5146-0.3232-0.4281-0.18080.04290.8944-0.7720.01570.98630.135-0.05480.4729-0.19130.1884-23.3014-12.94057.8887
285.64821.06313.7782.63253.48135.6870.36150.3352-1.22040.7781-0.57260.66151.0998-0.50810.21110.829-0.12380.16920.2275-0.26810.6487-17.6248-20.027317.7824
297.7521-6.3732.331210.4877-4.824712.74150.0758-0.227-0.57240.51840.06840.35120.34120.0874-0.14420.2681-0.0993-0.00220.28950.03180.1152-18.53340.960530.6469
300.9476.0151-8.522938.2123-54.145276.7218-0.43310.52840.304-1.82973.25461.89312.5813-4.8295-2.82150.55670.4057-0.14131.0645-0.00870.2811-29.600411.788819.0678
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 16
2X-RAY DIFFRACTION2A17 - 77
3X-RAY DIFFRACTION3A78 - 90
4X-RAY DIFFRACTION4A91 - 115
5X-RAY DIFFRACTION5A116 - 143
6X-RAY DIFFRACTION6B2 - 25
7X-RAY DIFFRACTION7B26 - 60
8X-RAY DIFFRACTION8B61 - 100
9X-RAY DIFFRACTION9B101 - 137
10X-RAY DIFFRACTION10B138 - 142
11X-RAY DIFFRACTION11C3 - 40
12X-RAY DIFFRACTION12C41 - 50
13X-RAY DIFFRACTION13C51 - 69
14X-RAY DIFFRACTION14C70 - 134
15X-RAY DIFFRACTION15C135 - 143
16X-RAY DIFFRACTION16D3 - 19
17X-RAY DIFFRACTION17D20 - 77
18X-RAY DIFFRACTION18D78 - 110
19X-RAY DIFFRACTION19D111 - 137
20X-RAY DIFFRACTION20D138 - 143
21X-RAY DIFFRACTION21E3 - 41
22X-RAY DIFFRACTION22E42 - 78
23X-RAY DIFFRACTION23E79 - 92
24X-RAY DIFFRACTION24E93 - 114
25X-RAY DIFFRACTION25E115 - 141
26X-RAY DIFFRACTION26F3 - 23
27X-RAY DIFFRACTION27F24 - 72
28X-RAY DIFFRACTION28F73 - 114
29X-RAY DIFFRACTION29F115 - 136
30X-RAY DIFFRACTION30F137 - 142

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