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- PDB-3pxp: Crystal structure of a PAS and DNA binding domain containing prot... -

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Basic information

Entry
Database: PDB / ID: 3pxp
TitleCrystal structure of a PAS and DNA binding domain containing protein (Caur_2278) from CHLOROFLEXUS AURANTIACUS J-10-FL at 2.30 A resolution
ComponentsHelix-turn-helix domain protein
KeywordsTRANSCRIPTION REGULATOR / DNA-BINDING / BASIC HELIX-LOOP-HELIX MOTIF / BHLH MOTIF / LAMBDA REPRESSOR-LIKE DNA-BINDING FOLD / PER ARNT SIM DOMAIN / PAS DOMAIN / PROFILIN-LIKE FOLD / TRANSCRIPTION / TRANSCRIPTION REGULATION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


Beta-Lactamase - #180 / MmyB-like transcription regulator ligand binding / MmyB-like transcription regulator ligand binding domain / Helix-turn-helix domain / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily ...Beta-Lactamase - #180 / MmyB-like transcription regulator ligand binding / MmyB-like transcription regulator ligand binding domain / Helix-turn-helix domain / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
MYRISTIC ACID / Helix-turn-helix domain protein
Similarity search - Component
Biological speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Plos One / Year: 2012
Title: Structure of an MmyB-Like Regulator from C. aurantiacus, Member of a New Transcription Factor Family Linked to Antibiotic Metabolism in Actinomycetes.
Authors: Xu, Q. / van Wezel, G.P. / Chiu, H.J. / Jaroszewski, L. / Klock, H.E. / Knuth, M.W. / Miller, M.D. / Lesley, S.A. / Godzik, A. / Elsliger, M.A. / Deacon, A.M. / Wilson, I.A.
History
DepositionDec 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Aug 15, 2012Group: Database references
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Helix-turn-helix domain protein
B: Helix-turn-helix domain protein
C: Helix-turn-helix domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,99421
Polymers103,5113
Non-polymers1,48318
Water10,953608
1
A: Helix-turn-helix domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0167
Polymers34,5041
Non-polymers5126
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Helix-turn-helix domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9546
Polymers34,5041
Non-polymers4505
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Helix-turn-helix domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0258
Polymers34,5041
Non-polymers5217
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Helix-turn-helix domain protein
B: Helix-turn-helix domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,97013
Polymers69,0072
Non-polymers96211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-12 kcal/mol
Surface area26040 Å2
MethodPISA
5
C: Helix-turn-helix domain protein
hetero molecules

C: Helix-turn-helix domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,04916
Polymers69,0072
Non-polymers1,04214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6800 Å2
ΔGint-48 kcal/mol
Surface area25070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.807, 83.568, 54.520
Angle α, β, γ (deg.)90.00, 103.12, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-909-

HOH

21C-924-

HOH

DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY PROVIDES SUPPORTING EVIDENCE THAT A MONOMER IS AN OLIGOMERIZATION STATE IN SOLUTION. CRYSTAL PACKING SUGGESTS A DIMER IS AN OLIGOMERIZATION STATE.

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Components

#1: Protein Helix-turn-helix domain protein


Mass: 34503.703 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aurantiacus (bacteria) / Strain: ATCC 29366 / DSM 635 / J-10-fl / Gene: Caur_2278 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A9WGF5
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.45 Å3/Da / Density % sol: 49.84 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
Crystal growTemperature: 277 K / pH: 9.1
Details: 0.2M sodium chloride, 10.5% polyethylene glycol 8000, 0.1M CHES pH 9.1, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97916
DetectorType: MAR MAR325 / Detector: CCD / Date: Feb 23, 2007 / Details: FLAT MIRROR (VERTICAL FOCUSING)
RadiationMonochromator: SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.3→29.748 Å / Num. obs: 44327 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.21 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 2.42
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.4 / % possible all: 98.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
BUSTER-TNTBUSTER 2.8.0refinement
XSCALEdata processing
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
autoSHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.3→29.75 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 0.37
Details: 1. 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 ...Details: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 4.ELECTRON DENSITY INDICATES THAT MYRISTIC ACID (MYR) IS FOUND IN THE SUBSTRATE-BINDING SITE OF EACH MONOMER. ITS IDENTITY IS TENTATIVELY ASSIGNED BASED ON DENSITY.
RfactorNum. reflection% reflection
Rfree0.206 2235 5.04 %
Rwork0.168 --
obs0.169 44326 -
Displacement parametersBiso mean: 38.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.1569 Å20 Å20.3835 Å2
2--2.0869 Å20 Å2
3----0.9301 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7093 0 93 608 7794
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017474HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9310129HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3541SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes175HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1112HARMONIC5
X-RAY DIFFRACTIONt_it7474HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion2.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion964SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9014SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2479 156 4.78 %
Rwork0.1856 3106 -
all0.1885 3262 -
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)
11.09890.71090.14621.14230.00710.22390.0001-0.0422-0.00710.00240.01810.0451-0.0309-0.0427-0.0183-0.02930.0122-0.0145-0.07140.005-0.050745.1523-9.307114.5234
21.87550.92050.67571.48320.05380.4679-0.0287-0.06890.0916-0.02730.06250.2028-0.0073-0.106-0.0338-0.0840.01190.0027-0.07710.0339-0.067331.140312.19961.2425
31.0130.7541-0.442.3971-0.84850.8793-0.00880.03050.08970.0896-0.0382-0.05830.00510.02740.047-0.0946-0.0007-0.0228-0.0770.0007-0.09895.295544.501117.6944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|0 - 301 }A0 - 301
2X-RAY DIFFRACTION2{ B|0 - 301 }B0 - 301
3X-RAY DIFFRACTION3{ C|0 - 301 }C0 - 301

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