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- PDB-3lwf: Crystal structure of Putative transcriptional regulator (NP_47088... -

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Basic information

Entry
Database: PDB / ID: 3lwf
TitleCrystal structure of Putative transcriptional regulator (NP_470886.1) from LISTERIA INNOCUA at 2.06 A resolution
ComponentsPutative transcriptional regulator
KeywordsTranscription regulator / Putative transcriptional regulator / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / DNA-binding / Transcriptional regulator
Function / homology
Function and homology information


Transcription regulator Rrf2-type, conserved site / Rrf2-type HTH domain signature. / Transcription regulator Rrf2 / Iron-dependent Transcriptional regulator / Rrf2-type HTH domain profile. / 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
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.06 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative transcriptional regulator (NP_470886.1) from LISTERIA INNOCUA at 2.06 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative transcriptional regulator
B: Putative transcriptional regulator
C: Putative transcriptional regulator
D: Putative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,74530
Polymers72,6714
Non-polymers2,07326
Water5,945330
1
A: Putative transcriptional regulator
hetero molecules

A: Putative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,94420
Polymers36,3362
Non-polymers1,60818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area8270 Å2
ΔGint-163 kcal/mol
Surface area14580 Å2
MethodPISA
2
B: Putative transcriptional regulator
D: Putative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,11412
Polymers36,3362
Non-polymers77910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint-144 kcal/mol
Surface area14120 Å2
MethodPISA
3
C: Putative transcriptional regulator
hetero molecules

C: Putative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,31716
Polymers36,3362
Non-polymers98114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area8390 Å2
ΔGint-171 kcal/mol
Surface area14470 Å2
MethodPISA
4
A: Putative transcriptional regulator
B: Putative transcriptional regulator
C: Putative transcriptional regulator
D: Putative transcriptional regulator
hetero molecules

A: Putative transcriptional regulator
B: Putative transcriptional regulator
C: Putative transcriptional regulator
D: Putative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,48960
Polymers145,3428
Non-polymers4,14752
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area40910 Å2
ΔGint-731 kcal/mol
Surface area48930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.961, 115.782, 75.927
Angle α, β, γ (deg.)90.00, 120.70, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-141-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A-1 - 140
2114B-1 - 140
3114C-1 - 140
4114D-1 - 140

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Components

#1: Protein
Putative transcriptional regulator / Lin1550 protein


Mass: 18167.801 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Gene: lin1550 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q92BJ8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.83 Å3/Da / Density % sol: 56.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.3
Details: 1.9500M ammonium sulfate, 0.2000M lithium sulfate, 0.1M CAPS pH 10.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97925,0.91837,0.97898
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 3, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979251
20.918371
30.978981
ReflectionResolution: 2.06→72.83 Å / Num. obs: 49880 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.087 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.62
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.06-2.130.6392176754716199.7
2.13-2.220.4882.7198385254199.5
2.22-2.320.3753.5186194933199.8
2.32-2.440.34.2184424869199.7
2.44-2.590.2335.3187154943199.6
2.59-2.790.1657.4189564999199.7
2.79-3.070.10510.9191055031199.4
3.07-3.520.06216.6192095066199.5
3.52-4.420.04124.1187344967199
4.42-72.830.03928.7187925087198.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.06→72.83 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 8.988 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.149
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. SULFATE (SO4) AND CHLORIDE (CL) MODELED WERE PRESENT IN CRYSTLLIZATION CONDITIONS OR IN PROTEIN BUFFER.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2529 5.1 %RANDOM
Rwork0.18 ---
obs0.182 49880 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.36 Å2 / Biso mean: 29.955 Å2 / Biso min: 8.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.21 Å20 Å2-0.23 Å2
2---1.02 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.06→72.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4461 0 102 330 4893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224719
X-RAY DIFFRACTIONr_bond_other_d0.0010.023171
X-RAY DIFFRACTIONr_angle_refined_deg1.4462.0036410
X-RAY DIFFRACTIONr_angle_other_deg0.89337774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5675606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33224.381210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67315867
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5381537
X-RAY DIFFRACTIONr_chiral_restr0.0860.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025184
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02885
X-RAY DIFFRACTIONr_mcbond_it1.8432891
X-RAY DIFFRACTIONr_mcbond_other0.77231205
X-RAY DIFFRACTIONr_mcangle_it3.0754666
X-RAY DIFFRACTIONr_scbond_it5.581828
X-RAY DIFFRACTIONr_scangle_it7.677111727
Refine LS restraints NCS

Ens-ID: 1 / Number: 1717 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.280.5
2BMEDIUM POSITIONAL0.310.5
3CMEDIUM POSITIONAL0.310.5
4DMEDIUM POSITIONAL0.260.5
1AMEDIUM THERMAL1.322
2BMEDIUM THERMAL1.092
3CMEDIUM THERMAL1.042
4DMEDIUM THERMAL1.162
LS refinement shellResolution: 2.06→2.113 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 193 -
Rwork0.256 3473 -
all-3666 -
obs--99.86 %
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)
10.59310.2157-0.63170.0955-0.15591.75630.0074-0.0101-0.0144-0.0356-0.019-0.0041-0.1777-0.00710.01170.09380.02980.00340.0167-0.00370.0057-59.585125.242913.768
20.87850.9678-0.23191.8472-0.16320.21540.0309-0.0579-0.0393-0.0319-0.0107-0.0328-0.03780.0749-0.02020.0386-0.0138-0.0090.0273-0.00870.0134-42.507712.351323.4166
31.0822-0.23120.61890.4423-0.21731.4226-0.01510.00960.0117-0.0061-0.0337-0.07490.07470.09610.04880.01240.01510.01020.02080.0170.0219-44.682-24.711910.5685
40.80060.6074-0.30781.2728-0.15920.6424-0.02240.0663-0.01240.00020.02590.0256-0.0529-0.0295-0.00350.01050.00150.00740.01270.00720.0151-56.9435-11.790526.2233
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 140
2X-RAY DIFFRACTION2B-3 - 140
3X-RAY DIFFRACTION3C-3 - 140
4X-RAY DIFFRACTION4D-3 - 140

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