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- PDB-3qi7: Crystal structure of a Putative transcriptional regulator (YP_001... -

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Basic information

Entry
Database: PDB / ID: 3qi7
TitleCrystal structure of a Putative transcriptional regulator (YP_001089212.1) from Clostridium difficile 630 at 1.86 A resolution
ComponentsPutative transcriptional regulator
KeywordsTRANSCRIPTION / PERIPLASMIC BINDING PROTEIN-LIKE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY / SUGAR BINDING PROTEIN
Function / homology
Function and homology information


Defensin A-like - #130 / Rossmann fold - #11390 / Rossmann fold - #11400 / Protein of unknown function DUF3798 / Protein of unknown function (DUF3798) / Defensin A-like / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 2-Layer Sandwich ...Defensin A-like - #130 / Rossmann fold - #11390 / Rossmann fold - #11400 / Protein of unknown function DUF3798 / Protein of unknown function (DUF3798) / Defensin A-like / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative transcriptional regulator (YP_001089212.1) from Clostridium difficile 630 at 1.86 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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
Revision 1.5Nov 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _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: Putative transcriptional regulator
B: Putative transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)84,9172
Polymers84,9172
Non-polymers00
Water10,088560
1
A: Putative transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)42,4581
Polymers42,4581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)42,4581
Polymers42,4581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.886, 102.479, 154.102
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEILEILE6AA339
21ILEILEILEILE6BB339
12ILEILELYSLYS2AA34 - 6810 - 44
22ILEILELYSLYS2BB34 - 6810 - 44
13ILEILELYSLYS4AA69 - 7845 - 54
23ILEILELYSLYS4BB69 - 7845 - 54
14VALVALLEULEU2AA79 - 8855 - 64
24VALVALLEULEU2BB79 - 8855 - 64
15PROPROASNASN4AA89 - 9565 - 71
25PROPROASNASN4BB89 - 9565 - 71
16ILEILELEULEU2AA96 - 29372 - 269
26ILEILELEULEU2BB96 - 29372 - 269
17LYSLYSGLNGLN4AA294 - 301270 - 277
27LYSLYSGLNGLN4BB294 - 301270 - 277
18ASNASNTYRTYR2AA302 - 395278 - 371
28ASNASNTYRTYR2BB302 - 395278 - 371
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Putative transcriptional regulator / Putative lipoprotein


Mass: 42458.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD2701 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q183D5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 26-395) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...THIS CONSTRUCT (RESIDUES 26-395) WAS EXPRESSED WITH AN N-TERMINAL 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.96
Details: 30.00% polyethylene glycol 4000, 0.20M ammonium acetate, 0.1M sodium acetate pH 4.96, Additive: 0.001 M spermine, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97936
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 5, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 1.86→48.622 Å / Num. obs: 68584 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.708 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 10.73
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.86-1.931.0411.654038971001100
1.93-20.7112.43503261401100
2-2.090.4833.53861067541100
2.09-2.20.3364.93918168541100
2.2-2.340.2486.53951069081100
2.34-2.520.1958.13916968391100
2.52-2.780.13411.5402857043199.9
2.78-3.180.09116389596843199.9
3.18-40.05623.4387046887199.5
4-48.620.0527.7386347215198.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
BP3phasing
XSCALEdata scaling
REFMAC5.5.0110refinement
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.86→48.622 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.23 / SU B: 6.322 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.13
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 RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 3468 5.1 %RANDOM
Rwork0.1897 ---
obs0.1913 68515 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.07 Å2 / Biso mean: 31.6134 Å2 / Biso min: 11.43 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å20 Å2
2---0.22 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.86→48.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5584 0 0 560 6144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225827
X-RAY DIFFRACTIONr_bond_other_d0.0010.023890
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.9817920
X-RAY DIFFRACTIONr_angle_other_deg0.89439693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4515761
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.58527.026269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.592151111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7371512
X-RAY DIFFRACTIONr_chiral_restr0.0810.2919
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216477
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02995
X-RAY DIFFRACTIONr_mcbond_it1.55233651
X-RAY DIFFRACTIONr_mcbond_other0.63331451
X-RAY DIFFRACTIONr_mcangle_it2.49355961
X-RAY DIFFRACTIONr_scbond_it4.25282176
X-RAY DIFFRACTIONr_scangle_it6.157111934
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1954TIGHT POSITIONAL0.220.05
2452MEDIUM POSITIONAL0.450.5
6LOOSE POSITIONAL1.55
1954TIGHT THERMAL0.970.5
2452MEDIUM THERMAL1.082
6LOOSE THERMAL0.8410
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 250 -
Rwork0.275 4758 -
all-5008 -
obs--99.94 %
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)
10.8103-0.14880.22110.7140.21770.84960.0799-0.1992-0.0133-0.0123-0.0025-0.00180.1013-0.0298-0.07750.0078-0.0241-0.02410.06120.01650.05439.029-8.95136.47
20.29520.05710.65540.96790.05721.97690.05290.0440.0848-0.1607-0.1199-0.09640.11810.12330.0670.02860.02880.03930.02380.01870.065134.9987.3465.387
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 395
2X-RAY DIFFRACTION2B33 - 395

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