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- PDB-3lte: CRYSTAL STRUCTURE OF RESPONSE REGULATOR (SIGNAL RECEIVER DOMAIN) ... -

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Basic information

Entry
Database: PDB / ID: 3lte
TitleCRYSTAL STRUCTURE OF RESPONSE REGULATOR (SIGNAL RECEIVER DOMAIN) FROM Bermanella marisrubri
ComponentsResponse regulator
KeywordsTRANSCRIPTION / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / NYSGRC / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


phosphorelay signal transduction system / DNA binding
Similarity search - Function
SinI-like, DNA-binding domain / Helix-turn-helix domain, group 17 / Helix-turn-helix domain / Transcriptional regulatory protein WalR-like / Putative DNA-binding domain superfamily / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily ...SinI-like, DNA-binding domain / Helix-turn-helix domain, group 17 / Helix-turn-helix domain / Transcriptional regulatory protein WalR-like / Putative DNA-binding domain superfamily / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Response regulator
Similarity search - Component
Biological speciesBermanella marisrubri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsPatskovsky, Y. / Toro, R. / Gilmore, M. / Miller, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF RESPONSE REGULATOR SIGNAL RECEIVER DOMAIN FROM Bermanella marisrubri RED65
Authors: Patskovsky, Y. / Toro, R. / Gilmore, M. / Miller, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator
B: Response regulator
C: Response regulator
D: Response regulator
E: Response regulator
F: Response regulator
G: Response regulator
H: Response regulator
I: Response regulator
J: Response regulator
K: Response regulator
L: Response regulator
M: Response regulator
N: Response regulator
O: Response regulator
P: Response regulator
Q: Response regulator
R: Response regulator
S: Response regulator
T: Response regulator
U: Response regulator
V: Response regulator
W: Response regulator
X: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,80927
Polymers357,52724
Non-polymers2823
Water11,890660
1
A: Response regulator
B: Response regulator


Theoretical massNumber of molelcules
Total (without water)29,7942
Polymers29,7942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-11 kcal/mol
Surface area12000 Å2
MethodPISA
2
C: Response regulator
D: Response regulator


Theoretical massNumber of molelcules
Total (without water)29,7942
Polymers29,7942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-11 kcal/mol
Surface area12100 Å2
MethodPISA
3
E: Response regulator
F: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8893
Polymers29,7942
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-15 kcal/mol
Surface area12760 Å2
MethodPISA
4
G: Response regulator
H: Response regulator


Theoretical massNumber of molelcules
Total (without water)29,7942
Polymers29,7942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-12 kcal/mol
Surface area12400 Å2
MethodPISA
5
I: Response regulator
J: Response regulator


Theoretical massNumber of molelcules
Total (without water)29,7942
Polymers29,7942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-11 kcal/mol
Surface area11770 Å2
MethodPISA
6
K: Response regulator
L: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8893
Polymers29,7942
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-17 kcal/mol
Surface area11950 Å2
MethodPISA
7
M: Response regulator
N: Response regulator


Theoretical massNumber of molelcules
Total (without water)29,7942
Polymers29,7942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-11 kcal/mol
Surface area11890 Å2
MethodPISA
8
O: Response regulator
P: Response regulator


Theoretical massNumber of molelcules
Total (without water)29,7942
Polymers29,7942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-13 kcal/mol
Surface area11940 Å2
MethodPISA
9
Q: Response regulator
R: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8863
Polymers29,7942
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-11 kcal/mol
Surface area11740 Å2
MethodPISA
10
S: Response regulator
T: Response regulator


Theoretical massNumber of molelcules
Total (without water)29,7942
Polymers29,7942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-12 kcal/mol
Surface area12130 Å2
MethodPISA
11
U: Response regulator
V: Response regulator


Theoretical massNumber of molelcules
Total (without water)29,7942
Polymers29,7942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-14 kcal/mol
Surface area11930 Å2
MethodPISA
12
W: Response regulator
X: Response regulator


Theoretical massNumber of molelcules
Total (without water)29,7942
Polymers29,7942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-11 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.707, 149.725, 281.071
Angle α, β, γ (deg.)90.00, 91.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ...
Response regulator


Mass: 14896.974 Da / Num. of mol.: 24 / Fragment: SIGNAL RECEIVER DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bermanella marisrubri (bacteria) / Gene: RED65_02614 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1N036
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 660 / 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: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M TRIS-HCL, PH 7.0, 2M AMMONIUM SULFATE, 200MM LITHIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 23, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 240435 / % possible obs: 100 % / Observed criterion σ(I): -5 / Redundancy: 3.2 % / Biso Wilson estimate: 34.725 Å2 / Rsym value: 0.093 / Net I/σ(I): 5.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 0.7 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXmodel building
RESOLVEmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.921 / SU B: 14.02 / SU ML: 0.17 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28157 6827 3 %RANDOM
Rwork0.23869 ---
obs0.23995 220599 94.74 %-
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: 23.943 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20 Å20.04 Å2
2---1.44 Å20 Å2
3---3.08 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22515 0 16 660 23191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02223098
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.97731270
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54652939
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.07325.4711104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.831154392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.00615154
X-RAY DIFFRACTIONr_chiral_restr0.0790.23669
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02117130
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.39214451
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.271323326
X-RAY DIFFRACTIONr_scbond_it2.8338647
X-RAY DIFFRACTIONr_scangle_it4.3657899
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 514 -
Rwork0.328 15929 -
obs--93.39 %
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)
12.8326-0.7013-0.20784.1299-0.06221.5054-0.0141-0.01810.1390.2615-0.0130.50280.1114-0.19260.02710.31690.00410.05620.26410.00060.2361-29.669933.8131124.4591
22.95310.2179-0.0612.9260.1991.61930.0023-0.022-0.12680.0914-0.0247-0.0667-0.0173-0.0130.02250.22980.01250.00170.19950.01320.0321-16.158610.2245120.3028
32.1645-0.63540.17433.69130.03742.57480.12920.01050.1637-0.1544-0.03960.0265-0.05530.1632-0.08970.29550.0015-0.00260.22550.03110.2123-27.190532.031487.3051
44.30.3041-0.51122.6781-0.3051.6352-0.0044-0.0199-0.2096-0.0896-0.07310.00710.05980.05630.07750.25910.0112-0.01760.1906-0.00040.0583-13.03598.459991.3188
52.81281.13390.3732.3902-0.35492.7871-0.03160.03310.0045-0.0810.022-0.14280.11750.14760.00960.2271-0.01460.040.1908-0.0090.113625.496728.883316.8701
63.3947-0.7037-0.0843.7104-0.08111.7302-0.04650.0097-0.1177-0.14350.01790.1217-0.0215-0.02230.02860.1853-0.00640.02240.1739-0.02080.087611.93884.899521.2628
72.6761-1.17040.21573.3049-0.16022.1005-0.0738-0.075-0.07460.12890.075-0.1494-0.14440.1653-0.00110.25170.0129-0.03470.21870.01410.1508-17.757415.786153.4334
83.46320.74130.42393.38050.00071.708-0.1007-0.01870.0560.11950.03320.1677-0.00390.00460.06750.19530.0072-0.00310.1639-0.00980.0242-31.206539.847949.187
93.3071-0.85860.14343.1361-0.18281.51230.08490.1006-0.3415-0.063-0.06990.01590.0837-0.1405-0.0150.25010.0316-0.00770.2441-0.02150.1633-17.579212.808516.2159
103.23860.0461-0.65462.84930.18861.2615-0.01340.07030.1332-0.0447-0.0622-0.00630.0762-0.04810.07560.1890.0183-0.00250.16350.01020.0162-31.396636.298120.1601
113.7921-0.0601-0.13371.7431-0.18752.13710.0249-0.02120.23310.0810.02510.0311-0.26110.0559-0.050.22030.00170.04360.20850.03220.1309-9.878757.519613.9206
121.84250.39030.34353.00790.01280.6741-0.02950.1157-0.2420.05760.0223-0.15870.0328-0.04110.00720.245-0.0203-0.00290.2555-0.01620.187816.619458.175921.4667
133.59681.1025-0.30012.9765-0.04661.76680.1266-0.21290.47230.0914-0.08380.1388-0.1041-0.14-0.04270.2591-0.02350.02490.2333-0.03340.176126.006631.751154.1888
143.70430.24120.23052.97840.21871.7114-0.0201-0.1254-0.1359-0.0114-0.02120.0398-0.0637-0.05660.04130.1886-0.008-0.00250.1530.01420.007912.20368.431750.1924
154.48210.6140.43081.2086-0.0112.03880.0508-0.2335-0.01780.00730.0262-0.1497-0.1854-0.0568-0.0770.28390.0079-0.01180.2811-0.02390.2175.708462.8509123.1979
162.7002-0.5835-0.00763.79930.30381.7202-0.0073-0.1528-0.1229-0.0143-0.06420.1743-0.0167-0.00280.07140.2228-0.00670.00920.2385-0.00270.0626-21.741763.265119.323
174.27940.3968-0.18781.99650.00641.3848-0.07560.1907-0.4078-0.02950.1195-0.39540.12150.0294-0.04380.2823-0.01130.00560.3102-0.04770.23528.524361.823486.3369
183.06450.3137-0.20253.4673-0.13361.3872-0.05710.03650.1177-0.0890.01870.20630.03210.04520.03840.20380.00530.00140.21660.0010.0178-18.483761.650690.5749
193.8095-0.26440.07092.75250.13062.58460.00050.0371-0.1731-0.11490.0262-0.05610.2270.0949-0.02670.1805-0.0123-0.03150.18050.01790.0532-9.969962.067256.5707
202.4362-0.0011-0.38293.0084-0.47371.0587-0.0692-0.10030.18360.06220.033-0.1526-0.0415-0.06930.03610.24430.01310.01530.2545-0.02440.186116.877761.43749.043
212.25160.37970.09153.4451-0.28052.2751-0.0401-0.1180.17750.09260.04680.0873-0.218-0.1547-0.00680.2608-0.00010.01140.22550.01420.078516.945215.857384.5213
222.622-0.23320.37112.14960.06181.26630.02160.01450.0114-0.0699-0.0324-0.25970.12010.05430.01080.3331-0.00190.00130.2396-0.02560.217529.697539.187491.7532
232.6050.70630.1233.46640.14892.37050.06530.1245-0.0322-0.0642-0.0119-0.19160.01840.2805-0.05340.2438-0.0081-0.00120.2273-0.00470.084812.965318.0841126.5592
242.61050.11650.08062.7987-0.53541.39620.0096-0.12610.19690.01690.00310.10680.0394-0.1429-0.01270.27-0.01740.03060.30170.00740.194126.801140.7838119.1547
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A68 - 185
2X-RAY DIFFRACTION2B66 - 185
3X-RAY DIFFRACTION3C67 - 185
4X-RAY DIFFRACTION4D63 - 185
5X-RAY DIFFRACTION5E63 - 185
6X-RAY DIFFRACTION6F63 - 185
7X-RAY DIFFRACTION7G66 - 186
8X-RAY DIFFRACTION8H63 - 185
9X-RAY DIFFRACTION9I68 - 186
10X-RAY DIFFRACTION10J66 - 185
11X-RAY DIFFRACTION11K66 - 185
12X-RAY DIFFRACTION12L67 - 184
13X-RAY DIFFRACTION13M67 - 184
14X-RAY DIFFRACTION14N67 - 185
15X-RAY DIFFRACTION15O68 - 184
16X-RAY DIFFRACTION16P63 - 185
17X-RAY DIFFRACTION17Q69 - 185
18X-RAY DIFFRACTION18R67 - 184
19X-RAY DIFFRACTION19S66 - 185
20X-RAY DIFFRACTION20T67 - 185
21X-RAY DIFFRACTION21U66 - 184
22X-RAY DIFFRACTION22V67 - 184
23X-RAY DIFFRACTION23W66 - 185
24X-RAY DIFFRACTION24X67 - 184

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