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- PDB-1xma: Structure of a transcriptional regulator from Clostridium thermoc... -

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Basic information

Entry
Database: PDB / ID: 1xma
TitleStructure of a transcriptional regulator from Clostridium thermocellum Cth-833
ComponentsPredicted transcriptional regulator
KeywordsTRANSCRIPTION / Clostridium thermocellum / transcriptional regulator / Southeast Collaboratory for Structural Genomics / SECSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


: / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / 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
: / : / Transcriptional regulator, PadR-like family
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SAD / sad / Resolution: 2.301 Å
AuthorsYang, H. / Chen, L. / Lee, D. / Habel, J. / Nguyen, J. / Chang, S.-H. / Kataeva, I. / Xu, H. / Chang, J. / Zhao, M. ...Yang, H. / Chen, L. / Lee, D. / Habel, J. / Nguyen, J. / Chang, S.-H. / Kataeva, I. / Xu, H. / Chang, J. / Zhao, M. / Horanyi, P. / Florence, Q. / Zhou, W. / Tempel, W. / Lin, D. / Praissman, J. / Zhang, H. / Arendall III, W.B. / Richardson, J.S. / Richardson, D.C. / Ljungdahl, L. / Liu, Z.-J. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Structure of a transcriptional regulator from Clostridium thermocellum Cth-833
Authors: Yang, H. / Chen, L. / Lee, D. / Habel, J. / Nguyen, J. / Chang, S.-H. / Kataeva, I. / Xu, H. / Chang, J. / Zhao, M. / Horanyi, P. / Florence, Q. / Zhou, W. / Tempel, W. / Lin, D. / ...Authors: Yang, H. / Chen, L. / Lee, D. / Habel, J. / Nguyen, J. / Chang, S.-H. / Kataeva, I. / Xu, H. / Chang, J. / Zhao, M. / Horanyi, P. / Florence, Q. / Zhou, W. / Tempel, W. / Lin, D. / Praissman, J. / Zhang, H. / Arendall III, W.B. / Richardson, J.S. / Richardson, D.C. / Ljungdahl, L. / Liu, Z.-J. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics
History
DepositionOct 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 18, 2020Group: Data collection / Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Predicted transcriptional regulator
B: Predicted transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,36019
Polymers33,5582
Non-polymers80217
Water72140
1
A: Predicted transcriptional regulator
hetero molecules

B: Predicted transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,36019
Polymers33,5582
Non-polymers80217
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_456x-1,y,z+11
Buried area3530 Å2
ΔGint-113 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.483, 52.160, 51.076
Angle α, β, γ (deg.)90.00, 92.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Predicted transcriptional regulator


Mass: 16779.014 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: 48858444, UniProt: A3DGR1*PLUS
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 13 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.8 Å3/Da / Density % sol: 31.81 %
Crystal growTemperature: 291 K / pH: 8.5
Details: 8.5% v/v isopropanol, 10% w/v PEG 4000, 15% v/v glycerol, 0.085M TRIS, modified microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 92 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 10985 / Rmerge(I) obs: 0.049
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.280.151143.8
2.28-2.370.17162.5
2.37-2.480.119179.5
2.48-2.610.105198.2
2.61-2.770.091100
2.77-2.990.0631100
2.99-3.290.0481100
3.29-3.760.047199.6
3.76-4.730.0371100
4.73-300.0441100

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Phasing

PhasingMethod: sad
Phasing MADD res high: 3 Å / D res low: 20 Å / FOM : 0.43 / Reflection: 4792
Phasing MAD shell
Resolution (Å)FOM Reflection
9.91-200.42267
6.56-9.910.51405
5.22-6.560.45522
4.46-5.220.46598
3.96-4.460.45661
3.6-3.960.39715
3.32-3.60.42777
3.09-3.320.38847
Phasing dmFOM : 0.58 / FOM acentric: 0.58 / FOM centric: 0.62 / Reflection: 10972 / Reflection acentric: 10282 / Reflection centric: 690
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.3-19.5560.920.920.8653044882
3.9-6.30.90.910.8416541512142
3.1-3.90.830.840.7120501915135
2.8-3.10.610.610.6320761963113
2.4-2.80.340.340.3633893233156
2.2-2.40.190.180.271273121162

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1data extraction
ISASphasing
RefinementMethod to determine structure: SAD / Resolution: 2.301→18.239 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.896 / Cross valid method: THROUGHOUT / ESU R: 0.4 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26676 518 5.1 %RANDOM
Rwork0.20534 ---
obs0.20853 9669 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.084 Å2
Baniso -1Baniso -2Baniso -3
1--0.072 Å20 Å20.024 Å2
2--0.033 Å20 Å2
3---0.041 Å2
Refinement stepCycle: LAST / Resolution: 2.301→18.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1698 0 17 40 1755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221748
X-RAY DIFFRACTIONr_bond_other_d00.021608
X-RAY DIFFRACTIONr_angle_refined_deg1.21.9782348
X-RAY DIFFRACTIONr_angle_other_deg3.79333745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2715200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4423.33381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42115345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2211512
X-RAY DIFFRACTIONr_chiral_restr0.0890.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021858
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02372
X-RAY DIFFRACTIONr_nbd_refined0.1930.2330
X-RAY DIFFRACTIONr_nbd_other0.2370.21274
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2836
X-RAY DIFFRACTIONr_nbtor_other0.1090.2810
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.251
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2570.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.0571.51007
X-RAY DIFFRACTIONr_mcbond_other01.5422
X-RAY DIFFRACTIONr_mcangle_it3.21621640
X-RAY DIFFRACTIONr_scbond_it2.3233741
X-RAY DIFFRACTIONr_scangle_it3.3244.5708
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.301→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 37 -
Rwork0.226 472 -
obs--100 %

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