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- PDB-7ff4: The crystal structure of Clostridium cellulolyticum LacI family t... -

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Basic information

Entry
Database: PDB / ID: 7ff4
TitleThe crystal structure of Clostridium cellulolyticum LacI family transcriptional regulator Ccel_1438
ComponentsTranscriptional regulator, LacI family
KeywordsTRANSCRIPTION / LacI family transcriptional regulator
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcriptional regulator LacI/GalR-like, sensor domain / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Periplasmic binding protein-like I
Similarity search - Domain/homology
Transcriptional regulator, LacI family
Similarity search - Component
Biological speciesRuminiclostridium cellulolyticum H10 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsZhang, N. / Ge, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970103 China
CitationJournal: To Be Published
Title: The crystal structure of Clostridium cellulolyticum LacI family transcriptional regulator Ccel_1438
Authors: Zhang, N. / Ge, H.
History
DepositionJul 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator, LacI family
B: Transcriptional regulator, LacI family
C: Transcriptional regulator, LacI family
D: Transcriptional regulator, LacI family


Theoretical massNumber of molelcules
Total (without water)154,3234
Polymers154,3234
Non-polymers00
Water4,414245
1
A: Transcriptional regulator, LacI family
B: Transcriptional regulator, LacI family


Theoretical massNumber of molelcules
Total (without water)77,1612
Polymers77,1612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-19 kcal/mol
Surface area23240 Å2
MethodPISA
2
C: Transcriptional regulator, LacI family

D: Transcriptional regulator, LacI family


Theoretical massNumber of molelcules
Total (without water)77,1612
Polymers77,1612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_444-y-2/3,x-y-1/3,z-1/31
Buried area3590 Å2
ΔGint-21 kcal/mol
Surface area23630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.518, 194.518, 118.640
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 60 through 337)
21chain B
31(chain C and resid 60 through 337)
41(chain D and resid 60 through 337)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 60 - 337 / Label seq-ID: 60 - 337

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 60 through 337)AA
2chain BBB
3(chain C and resid 60 through 337)CC
4(chain D and resid 60 through 337)DD

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Components

#1: Protein
Transcriptional regulator, LacI family


Mass: 38580.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminiclostridium cellulolyticum H10 (bacteria)
Strain: H10 / Gene: Ccel_1438 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B8I1W6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis Tris Propane pH 6.5, 0.2 M Trisodium citrate dihydrate, 20% w/v PEG 3350, 12% v/v Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.19→48.64 Å / Num. obs: 85663 / % possible obs: 99.5 % / Redundancy: 9.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Net I/σ(I): 18.6
Reflection shellResolution: 2.19→2.27 Å / Rmerge(I) obs: 0.76 / Num. unique obs: 8185 / CC1/2: 0.742

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RZR

1rzr


Resolution: 2.19→48.629 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 4310 5.03 %
Rwork0.1778 81316 -
obs0.1793 85626 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 199.83 Å2 / Biso mean: 60.7669 Å2 / Biso min: 29.72 Å2
Refinement stepCycle: final / Resolution: 2.19→48.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8792 0 0 245 9037
Biso mean---56.15 -
Num. residues----1117
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3364X-RAY DIFFRACTION7.988TORSIONAL
12B3364X-RAY DIFFRACTION7.988TORSIONAL
13C3364X-RAY DIFFRACTION7.988TORSIONAL
14D3364X-RAY DIFFRACTION7.988TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1902-2.21510.30011120.2779256793
2.2151-2.24120.2834980.2685264296
2.2412-2.26850.29461340.2592262897
2.2685-2.29720.26751870.248266799
2.2972-2.32740.29591490.2385274899
2.3274-2.35930.28171820.23572636100
2.3593-2.3930.25561490.22642730100
2.393-2.42870.27121620.22452726100
2.4287-2.46670.22371590.2052696100
2.4667-2.50710.25421610.20092693100
2.5071-2.55040.2421900.19942694100
2.5504-2.59670.2411560.21152725100
2.5967-2.64670.26061380.20572767100
2.6467-2.70070.25781130.20832747100
2.7007-2.75940.24711810.21292666100
2.7594-2.82360.27571150.20062760100
2.8236-2.89420.2602600.2072800100
2.8942-2.97240.23381420.20672735100
2.9724-3.05990.22181740.20712693100
3.0599-3.15860.22231580.20122687100
3.1586-3.27150.23141240.20632772100
3.2715-3.40250.23011100.1922796100
3.4025-3.55730.19821660.17642667100
3.5573-3.74480.18781740.16322717100
3.7448-3.97930.1831520.16012691100
3.9793-4.28630.17251170.14572767100
4.2863-4.71740.17251770.13582688100
4.7174-5.39920.18151120.14962768100
5.3992-6.79950.21671180.18422728100
6.7995-480.16081400.1448271599
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)
10.568-0.4810.25190.5406-0.0430.302-0.08120.27840.11490.06650.28930.32660.00340.14620.00220.4248-0.02640.03210.4552-0.01330.5464-33.1417-15.083122.334
22.0938-0.04810.60711.2509-0.48170.6534-0.19610.58620.1613-0.16460.1117-0.2844-0.03370.2068-0.00020.4054-0.08860.08290.50430.02630.4033-23.1804-13.480913.9042
31.34940.5208-0.16032.19790.85731.8407-0.03330.17750.0377-0.1910.1413-0.0474-0.18720.03570.00030.40810.02780.0440.3924-0.02440.3178-39.0822-39.38128.3223
4-0.00860.0902-0.0510.5931-0.02480.38150.03850.0309-0.1520.10790.0466-0.17670.02830.06850.00010.36780.010.03930.3739-0.02860.4326-28.1084-28.054423.6174
53.5227-1.07111.70560.6984-0.08051.1363-0.4263-0.20120.51750.11890.07170.0747-0.1125-0.2251-0.0020.49960.0247-0.05610.3877-0.05030.5756-44.6393-1.696820.6293
60.897-0.2173-0.1780.5121-0.36770.39580.08270.09460.23690.0404-0.0087-0.0328-0.1426-0.173-0.00060.38660.0594-0.00560.48640.02180.3838-70.0209-13.152612.1504
71.1268-0.1405-0.06061.9988-0.49041.1995-0.0889-0.1966-0.44790.10910.0022-0.24520.05880.0421-0.00040.37440.036-0.01750.45660.03940.4658-63.7913-24.573513.1959
81.5118-0.60850.24410.4386-0.39470.4137-0.16260.35180.48930.0067-0.0256-0.1383-0.0896-0.0644-0.00270.4550.0131-0.03050.42050.09220.53-53.8375-2.81927.6873
90.64140.19680.44410.4770.3460.3939-0.14620.02320.168-0.13170.30090.10730.0591-0.0314-0.00020.4899-0.074-0.12330.41780.00380.5203-44.4471-73.935130.4982
100.70240.15550.72130.56420.62821.13420.2593-0.2897-0.14940.3602-0.1701-0.09020.2246-0.34130.00110.5326-0.0735-0.1520.51660.05350.4264-44.0825-74.443444.5409
111.5866-0.87720.00182.73850.13161.85790.0173-0.0253-0.19330.21430.01260.36570.0558-0.1924-0.00050.4165-0.04310.01320.39050.00020.3916-54.275-46.660235.1871
120.26570.30420.12540.46840.41270.4790.10390.0326-0.0806-0.01310.0655-0.1945-0.0223-0.0008-0.00050.3879-0.0209-0.09760.3422-0.02220.4087-37.2989-60.695434.0421
130.0882-0.0324-0.0980.6384-0.48660.46820.02880.1583-0.20810.0496-0.0063-0.1473-0.20270.01560.00050.53670.06260.07490.45730.1070.5351-42.2156-24.636567.0276
140.7662-0.86840.14261.18510.1340.9743-0.05130.0106-0.1557-0.36730.1670.47660.0218-0.1360.00110.52070.0456-0.06780.37450.07660.5251-49.5387-23.802855.4377
150.3989-0.2616-0.74070.58890.16361.5730.08590.0729-0.0296-0.1315-0.08470.0814-0.15180.151900.5432-0.03560.00460.46340.07190.5197-22.9108-15.725245.1473
160.8169-0.23790.10491.1155-0.28552.6526-0.183-0.1838-0.31660.0279-0.12290.07580.86670.7552-0.00090.64160.1540.06440.55560.10590.5509-16.8215-25.698350.1649
170.2576-0.52740.39741.089-0.75311.22580.0334-0.1290.10540.30870.00360.0513-0.30080.24890.00120.5501-0.0148-0.01190.39010.01060.4402-35.2197-12.668160.0658
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 58 through 88 )A58 - 88
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 160 )A89 - 160
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 295 )A161 - 295
4X-RAY DIFFRACTION4chain 'A' and (resid 296 through 337 )A296 - 337
5X-RAY DIFFRACTION5chain 'B' and (resid 60 through 160 )B60 - 160
6X-RAY DIFFRACTION6chain 'B' and (resid 161 through 206 )B161 - 206
7X-RAY DIFFRACTION7chain 'B' and (resid 207 through 295 )B207 - 295
8X-RAY DIFFRACTION8chain 'B' and (resid 296 through 337 )B296 - 337
9X-RAY DIFFRACTION9chain 'C' and (resid 59 through 100 )C59 - 100
10X-RAY DIFFRACTION10chain 'C' and (resid 101 through 160 )C101 - 160
11X-RAY DIFFRACTION11chain 'C' and (resid 161 through 295 )C161 - 295
12X-RAY DIFFRACTION12chain 'C' and (resid 296 through 337 )C296 - 337
13X-RAY DIFFRACTION13chain 'D' and (resid 58 through 100 )D58 - 100
14X-RAY DIFFRACTION14chain 'D' and (resid 101 through 160 )D101 - 160
15X-RAY DIFFRACTION15chain 'D' and (resid 161 through 205 )D161 - 205
16X-RAY DIFFRACTION16chain 'D' and (resid 206 through 295 )D206 - 295
17X-RAY DIFFRACTION17chain 'D' and (resid 296 through 337 )D296 - 337

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