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- PDB-5v5t: Crystal structure of leucine-rich protein regulator, ElrR, from E... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5v5t
TitleCrystal structure of leucine-rich protein regulator, ElrR, from Enterococcus faecalis
ComponentsConserved domain protein
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATOR
Function / homologyTranscriptional regulator
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SAD, MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsDe Groote, M.C.R. / Camargo, I.L. / Serror, P. / Horjales, E.
Funding support Brazil, France, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2013/26313-5 Brazil
USP/COFECUB International agreement2012-22 France
CitationJournal: To be published
Title: Crystal structure and functional characterization of ElrR, a member of the RRNPP family of transcriptional regulators.
Authors: De Groote, M.C.R. / Camargo, I.L. / Repoila, F. / Horjales, E. / Serror, P.
History
DepositionMar 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conserved domain protein
B: Conserved domain protein
C: Conserved domain protein
D: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,9805
Polymers144,8624
Non-polymers1181
Water3,333185
1
A: Conserved domain protein
D: Conserved domain protein


Theoretical massNumber of molelcules
Total (without water)72,4312
Polymers72,4312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-55 kcal/mol
Surface area28110 Å2
MethodPISA
2
B: Conserved domain protein
C: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5493
Polymers72,4312
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-45 kcal/mol
Surface area27950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.800, 75.330, 85.280
Angle α, β, γ (deg.)112.990, 89.930, 103.880
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 9:37 or resseq 39:44 or resid...
21(chain B and (resseq 9:37 or resseq 39:44 or resseq...
31(chain C and (resseq 9:37 or resseq 39:44 or resseq...
41(chain D and (resseq 9:37 or resseq 39:44 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 9:37 or resseq 39:44 or resid...A9 - 37
121(chain A and (resseq 9:37 or resseq 39:44 or resid...A39 - 44
131(chain A and (resseq 9:37 or resseq 39:44 or resid...A46
141(chain A and (resseq 9:37 or resseq 39:44 or resid...A48
151(chain A and (resseq 9:37 or resseq 39:44 or resid...A50 - 66
161(chain A and (resseq 9:37 or resseq 39:44 or resid...A68 - 69
171(chain A and (resseq 9:37 or resseq 39:44 or resid...A72 - 75
181(chain A and (resseq 9:37 or resseq 39:44 or resid...A77 - 82
191(chain A and (resseq 9:37 or resseq 39:44 or resid...A84 - 92
1101(chain A and (resseq 9:37 or resseq 39:44 or resid...A94
1111(chain A and (resseq 9:37 or resseq 39:44 or resid...A97 - 110
1121(chain A and (resseq 9:37 or resseq 39:44 or resid...A112 - 134
1131(chain A and (resseq 9:37 or resseq 39:44 or resid...A136 - 157
1141(chain A and (resseq 9:37 or resseq 39:44 or resid...A159 - 171
1151(chain A and (resseq 9:37 or resseq 39:44 or resid...A173 - 194
1161(chain A and (resseq 9:37 or resseq 39:44 or resid...A196
1171(chain A and (resseq 9:37 or resseq 39:44 or resid...A199 - 226
1181(chain A and (resseq 9:37 or resseq 39:44 or resid...A228 - 232
1191(chain A and (resseq 9:37 or resseq 39:44 or resid...A234 - 263
1201(chain A and (resseq 9:37 or resseq 39:44 or resid...A265
1211(chain A and (resseq 9:37 or resseq 39:44 or resid...A267 - 271
1221(chain A and (resseq 9:37 or resseq 39:44 or resid...A274 - 283
1231(chain A and (resseq 9:37 or resseq 39:44 or resid...A285 - 301
1241(chain A and (resseq 9:37 or resseq 39:44 or resid...A303 - 305
211(chain B and (resseq 9:37 or resseq 39:44 or resseq...B9 - 37
221(chain B and (resseq 9:37 or resseq 39:44 or resseq...B39 - 44
231(chain B and (resseq 9:37 or resseq 39:44 or resseq...B46
241(chain B and (resseq 9:37 or resseq 39:44 or resseq...B48
251(chain B and (resseq 9:37 or resseq 39:44 or resseq...B50 - 66
261(chain B and (resseq 9:37 or resseq 39:44 or resseq...B68 - 69
271(chain B and (resseq 9:37 or resseq 39:44 or resseq...B72 - 75
281(chain B and (resseq 9:37 or resseq 39:44 or resseq...B77 - 82
291(chain B and (resseq 9:37 or resseq 39:44 or resseq...B84 - 92
2101(chain B and (resseq 9:37 or resseq 39:44 or resseq...B94
2111(chain B and (resseq 9:37 or resseq 39:44 or resseq...B97 - 110
2121(chain B and (resseq 9:37 or resseq 39:44 or resseq...B112 - 134
2131(chain B and (resseq 9:37 or resseq 39:44 or resseq...B136 - 157
2141(chain B and (resseq 9:37 or resseq 39:44 or resseq...B159 - 171
2151(chain B and (resseq 9:37 or resseq 39:44 or resseq...B173 - 194
2161(chain B and (resseq 9:37 or resseq 39:44 or resseq...B196
2171(chain B and (resseq 9:37 or resseq 39:44 or resseq...B199 - 226
2181(chain B and (resseq 9:37 or resseq 39:44 or resseq...B228 - 232
2191(chain B and (resseq 9:37 or resseq 39:44 or resseq...B234 - 263
2201(chain B and (resseq 9:37 or resseq 39:44 or resseq...B265
2211(chain B and (resseq 9:37 or resseq 39:44 or resseq...B267 - 271
2221(chain B and (resseq 9:37 or resseq 39:44 or resseq...B274 - 283
2231(chain B and (resseq 9:37 or resseq 39:44 or resseq...B285 - 301
2241(chain B and (resseq 9:37 or resseq 39:44 or resseq...B303 - 305
311(chain C and (resseq 9:37 or resseq 39:44 or resseq...C9 - 37
321(chain C and (resseq 9:37 or resseq 39:44 or resseq...C39 - 44
331(chain C and (resseq 9:37 or resseq 39:44 or resseq...C46
341(chain C and (resseq 9:37 or resseq 39:44 or resseq...C48
351(chain C and (resseq 9:37 or resseq 39:44 or resseq...C50 - 66
361(chain C and (resseq 9:37 or resseq 39:44 or resseq...C68 - 69
371(chain C and (resseq 9:37 or resseq 39:44 or resseq...C72 - 75
381(chain C and (resseq 9:37 or resseq 39:44 or resseq...C77 - 82
391(chain C and (resseq 9:37 or resseq 39:44 or resseq...C84 - 92
3101(chain C and (resseq 9:37 or resseq 39:44 or resseq...C94
3111(chain C and (resseq 9:37 or resseq 39:44 or resseq...C97 - 110
3121(chain C and (resseq 9:37 or resseq 39:44 or resseq...C112 - 134
3131(chain C and (resseq 9:37 or resseq 39:44 or resseq...C136 - 157
3141(chain C and (resseq 9:37 or resseq 39:44 or resseq...C159 - 171
3151(chain C and (resseq 9:37 or resseq 39:44 or resseq...C173 - 194
3161(chain C and (resseq 9:37 or resseq 39:44 or resseq...C196
3171(chain C and (resseq 9:37 or resseq 39:44 or resseq...C199 - 226
3181(chain C and (resseq 9:37 or resseq 39:44 or resseq...C228 - 232
3191(chain C and (resseq 9:37 or resseq 39:44 or resseq...C234 - 263
3201(chain C and (resseq 9:37 or resseq 39:44 or resseq...C265
3211(chain C and (resseq 9:37 or resseq 39:44 or resseq...C267 - 271
3221(chain C and (resseq 9:37 or resseq 39:44 or resseq...C274 - 283
3231(chain C and (resseq 9:37 or resseq 39:44 or resseq...C285 - 301
3241(chain C and (resseq 9:37 or resseq 39:44 or resseq...C303 - 305
411(chain D and (resseq 9:37 or resseq 39:44 or resseq...D9 - 37
421(chain D and (resseq 9:37 or resseq 39:44 or resseq...D39 - 44
431(chain D and (resseq 9:37 or resseq 39:44 or resseq...D46
441(chain D and (resseq 9:37 or resseq 39:44 or resseq...D48
451(chain D and (resseq 9:37 or resseq 39:44 or resseq...D50 - 66
461(chain D and (resseq 9:37 or resseq 39:44 or resseq...D68 - 69
471(chain D and (resseq 9:37 or resseq 39:44 or resseq...D72 - 75
481(chain D and (resseq 9:37 or resseq 39:44 or resseq...D77 - 82
491(chain D and (resseq 9:37 or resseq 39:44 or resseq...D84 - 92
4101(chain D and (resseq 9:37 or resseq 39:44 or resseq...D94
4111(chain D and (resseq 9:37 or resseq 39:44 or resseq...D97 - 110
4121(chain D and (resseq 9:37 or resseq 39:44 or resseq...D112 - 134
4131(chain D and (resseq 9:37 or resseq 39:44 or resseq...D136 - 157
4141(chain D and (resseq 9:37 or resseq 39:44 or resseq...D159 - 171
4151(chain D and (resseq 9:37 or resseq 39:44 or resseq...D173 - 194
4161(chain D and (resseq 9:37 or resseq 39:44 or resseq...D196
4171(chain D and (resseq 9:37 or resseq 39:44 or resseq...D199 - 226
4181(chain D and (resseq 9:37 or resseq 39:44 or resseq...D228 - 232
4191(chain D and (resseq 9:37 or resseq 39:44 or resseq...D234 - 263
4201(chain D and (resseq 9:37 or resseq 39:44 or resseq...D265
4211(chain D and (resseq 9:37 or resseq 39:44 or resseq...D267 - 271
4221(chain D and (resseq 9:37 or resseq 39:44 or resseq...D274 - 283
4231(chain D and (resseq 9:37 or resseq 39:44 or resseq...D285 - 301
4241(chain D and (resseq 9:37 or resseq 39:44 or resseq...D303 - 305

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Components

#1: Protein
Conserved domain protein


Mass: 36215.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (strain ATCC 700802 / V583) (bacteria)
Strain: ATCC 700802 / V583 / Gene: EF_2687 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q830T5
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 1000, PEG 3350, MPD, MOPS/HEPES-Na, L-glutamate, DL-alanine, glycine, DL-lysine, DL-serine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→36.55 Å / Num. all: 76473 / Num. obs: 76473 / % possible obs: 89.8 % / Redundancy: 2.4 % / Biso Wilson estimate: 54.7 Å2 / Rpim(I) all: 0.039 / Rrim(I) all: 0.062 / Rsym value: 0.047 / Net I/av σ(I): 8.6 / Net I/σ(I): 9.3 / Num. measured all: 185116
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.4 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.15-2.270.5421.21791775520.4470.7050.5421.660.7
2.27-2.40.4961.425893107770.4090.6450.4961.791.7
2.4-2.570.2672.825178103530.220.3470.267393.5
2.57-2.780.1644.52362997120.1350.2130.1644.794.3
2.78-3.040.10172179889780.0830.1310.1017.594.8
3.04-3.40.05711.91997282160.0470.0750.05712.295.6
3.4-3.930.0416.21773272960.0330.0520.0417.496.3
3.93-4.810.03317.21495561490.0270.0430.03321.596.9
4.81-6.80.03515.91169748130.0280.0450.03522.397.5
6.8-36.550.02418.9634526270.0190.0310.02425.297.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.65 Å36.55 Å
Translation4.65 Å36.55 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
SCALA3.3.21data scaling
PHASER2.5.6model building
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT / Resolution: 2.15→36.55 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 5800 7.59 %
Rwork0.1957 70598 -
obs0.1992 76398 89.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 225.95 Å2 / Biso mean: 80.2784 Å2 / Biso min: 30.02 Å2
Refinement stepCycle: final / Resolution: 2.15→36.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9981 0 8 185 10174
Biso mean--86.25 62.54 -
Num. residues----1213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910224
X-RAY DIFFRACTIONf_angle_d1.1413790
X-RAY DIFFRACTIONf_chiral_restr0.0641562
X-RAY DIFFRACTIONf_plane_restr0.0071754
X-RAY DIFFRACTIONf_dihedral_angle_d20.0816296
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4879X-RAY DIFFRACTION14.807TORSIONAL
12B4879X-RAY DIFFRACTION14.807TORSIONAL
13C4879X-RAY DIFFRACTION14.807TORSIONAL
14D4879X-RAY DIFFRACTION14.807TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.17450.42261020.35341312141450
2.1745-2.20.3851120.34681440155255
2.2-2.22690.36571320.33441606173862
2.2269-2.25510.44911590.36951807196669
2.2551-2.28470.33491730.32632146231981
2.2847-2.3160.35131760.31742461263793
2.316-2.34910.34812030.29972466266993
2.3491-2.38420.34472040.28732395259993
2.3842-2.42140.30922190.26672414263393
2.4214-2.46110.31222110.27232463267493
2.4611-2.50350.2862210.2532426264793
2.5035-2.5490.32672080.25982443265194
2.549-2.59810.29871930.25312483267694
2.5981-2.65110.31131820.25522477265994
2.6511-2.70870.30452100.24522505271595
2.7087-2.77170.30272310.23172408263994
2.7717-2.8410.28481890.24122527271694
2.841-2.91780.28751820.24652490267295
2.9178-3.00360.29532050.25122508271395
3.0036-3.10050.30011950.2432510270595
3.1005-3.21120.27851990.2352502270196
3.2112-3.33970.25752230.21922490271396
3.3397-3.49160.27092160.21332513272996
3.4916-3.67550.24672120.20392511272396
3.6755-3.90560.24232400.18982507274796
3.9056-4.20670.22262070.17172516272397
4.2067-4.62930.18662080.14872566277497
4.6293-5.29740.1922020.13842558276097
5.2974-6.66760.21851900.16692564275498
6.6676-36.55490.16711960.14712584278097
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)
11.11150.0191-0.26770.1309-0.61013.14240.06190.2736-0.3714-0.29380.13280.42650.8615-2.01180.00490.4912-0.12-0.03161.40570.26840.7768-95.33884.8061-70.8394
20.9436-1.4009-1.1041.97361.52171.1261-0.4079-0.43310.23080.15640.7604-0.1730.2604-0.20450.02640.7074-0.07560.03480.80130.16930.6122-78.170276.5403-72.9624
31.36470.84560.15161.71320.73234.42530.0197-0.1508-0.0225-0.01850.0266-0.1576-0.09010.7014-0.02160.34-0.01260.03720.54280.1090.4386-51.286187.9067-81.4474
42.33290.33071.47132.6673-1.42031.9059-0.1208-0.37040.30720.3849-0.199-0.8412-0.63780.5130.11580.5124-0.0637-0.00070.7660.09990.6839-9.390568.3216-31.4779
51.0236-1.43420.03841.6848-0.0229-0.0415-0.4495-0.6719-0.31510.4170.32070.2748-0.5282-0.26580.16910.91790.2233-0.03681.02860.00790.6029-26.468676.2774-26.6361
62.16450.69-0.11523.6441-1.24731.2545-0.0486-0.1083-0.1066-0.08690.25420.32530.0255-0.2576-0.08010.3714-0.018-0.01210.5061-0.00170.3303-53.3174.1449-40.847
73.52220.15920.56941.2149-1.19122.4020.470.98470.9794-0.1526-0.7843-1.0190.49740.8157-0.05950.53410.0490.00090.85310.25850.8541-16.764883.3-45.1862
80.2078-0.58710.09251.5483-0.0723-0.0174-0.030.79020.36490.21530.1086-0.19871.0342-0.45460.20941.2439-0.0913-0.02310.9257-0.0660.6871-22.656863.889-49.2064
93.58280.8187-1.6241.6454-0.58591.5896-0.44450.0995-0.5238-0.27670.0749-0.21790.40480.09130.12320.5446-0.02740.09370.412-0.01590.5259-42.124347.7442-31.6863
102.68580.5219-0.09050.8809-0.75132.64760.58810.87870.4910.0521-0.09860.3918-0.3386-1.3367-0.1460.5354-0.01540.01621.09970.21010.6968-87.948784.9014-91.116
110.0605-0.4082-0.392.21231.91061.61070.12250.6181-0.00950.39790.0402-0.0175-0.4924-0.322-0.10920.98740.10790.07170.97270.15520.8082-81.5182100.5444-79.7352
122.7005-0.65510.76791.6479-0.40372.638-0.1035-0.00920.14690.16820.249-0.0295-0.5235-0.1655-0.06410.5050.02270.0510.42420.00430.4496-62.274799.0232-55.793
133.1691-0.5695-1.50651.84270.90292.5923-0.29560.0821-0.7579-0.0670.1520.18551.0183-0.50260.0060.747-0.1967-0.00730.53070.08080.5882-70.689568.0577-87.2212
144.0576-1.35320.66852.9409-0.64431.2272-0.3896-0.99361.10490.93670.1894-0.4715-0.70670.06560.05190.7609-0.0113-0.19080.7137-0.22240.6425-33.979892.3745-30.3838
153.22960.274-1.58392.7856-1.0261.1728-0.61850.4865-1.1574-1.11060.1633-0.63810.86470.27610.17890.973-0.06250.32370.6663-0.17520.8315-15.989247.4141-45.1235
162.36420.1521.0021.96420.77751.8946-0.1590.13760.6292-0.14130.22260.4631-0.9904-0.8883-0.07740.81140.3710.10570.81560.24020.6408-88.053109.1233-65.0927
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 61 )A3 - 61
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 94 )A62 - 94
3X-RAY DIFFRACTION3chain 'A' and (resid 170 through 308 )A170 - 308
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 61 )B4 - 61
5X-RAY DIFFRACTION5chain 'B' and (resid 62 through 94 )B62 - 94
6X-RAY DIFFRACTION6chain 'B' and (resid 170 through 308 )B170 - 308
7X-RAY DIFFRACTION7chain 'C' and (resid 8 through 61 )C8 - 61
8X-RAY DIFFRACTION8chain 'C' and (resid 62 through 94 )C62 - 94
9X-RAY DIFFRACTION9chain 'C' and (resid 170 through 307 )C170 - 307
10X-RAY DIFFRACTION10chain 'D' and (resid 8 through 61 )D8 - 61
11X-RAY DIFFRACTION11chain 'D' and (resid 62 through 94 )D62 - 94
12X-RAY DIFFRACTION12chain 'D' and (resid 170 through 308 )D170 - 308
13X-RAY DIFFRACTION13chain 'A' and (resid 95 through 169 )A95 - 169
14X-RAY DIFFRACTION14chain 'B' and (resid 95 through 169 )B95 - 169
15X-RAY DIFFRACTION15chain 'C' and (resid 95 through 169 )C95 - 169
16X-RAY DIFFRACTION16chain 'D' and (resid 95 through 169 )D95 - 169

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