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- PDB-3ctp: Crystal structure of periplasmic binding protein/LacI transcripti... -

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Basic information

Entry
Database: PDB / ID: 3ctp
TitleCrystal structure of periplasmic binding protein/LacI transcriptional regulator from Alkaliphilus metalliredigens QYMF complexed with D-xylulofuranose
ComponentsPeriplasmic binding protein/LacI transcriptional regulator
KeywordsTRANSCRIPTION REGULATOR / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / NYSGXRC / transcriptional regulator / L-xylulose / D-xylulofuranose / DNA-binding / Transcription regulation / PSI-2
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
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 / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-xylulofuranose / Periplasmic binding protein/LacI transcriptional regulator
Similarity search - Component
Biological speciesAlkaliphilus metalliredigens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.41 Å
AuthorsMalashkevich, V.N. / Toro, R. / Wasserman, S.R. / Meyer, A. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of periplasmic binding protein/LacI transcriptional regulator from Alkaliphilus metalliredigens QYMF complexed with L-xylulose.
Authors: Malashkevich, V.N. / Toro, R. / Wasserman, S.R. / Meyer, A. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionApr 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_asym_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / chem_comp / citation_author
Item: _audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms / _citation_author.identifier_ORCID
Revision 2.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic binding protein/LacI transcriptional regulator
B: Periplasmic binding protein/LacI transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1016
Polymers74,7552
Non-polymers3464
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-19.1 kcal/mol
Surface area20920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.172, 61.903, 74.362
Angle α, β, γ (deg.)90.000, 104.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Periplasmic binding protein/LacI transcriptional regulator


Mass: 37377.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alkaliphilus metalliredigens (bacteria)
Strain: QYMF / Gene: Amet_0586 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: A6TKU5
#2: Sugar ChemComp-XLF / beta-D-xylulofuranose / beta-D-xylulose / D-xylulose / xylulose / Xylulose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O5
IdentifierTypeProgram
DXulfbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylulofuranoseCOMMON NAMEGMML 1.0
b-D-XulfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 1.91 Å3/Da / Density % sol: 35.61 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes pH 7.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9798 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionRedundancy: 3.5 % / Av σ(I) over netI: 7.8 / Number: 713527 / Rmerge(I) obs: 0.076 / Χ2: 1.37 / D res high: 1.41 Å / D res low: 50 Å / Num. obs: 206130 / % possible obs: 96.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.045099.410.0493.0523.9
2.413.0410010.0651.9033.9
2.112.4110010.0791.4013.9
1.912.1110010.1091.0633.9
1.781.9110010.1680.8463.8
1.671.7810010.2480.7193.8
1.591.6799.710.310.6423.5
1.521.5998.410.390.6363.1
1.461.5296.610.5470.7982.6
1.411.4672.214.3451.8
ReflectionResolution: 1.41→50 Å / Num. obs: 206130 / % possible obs: 96.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.076 / Χ2: 1.368 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
1.41-1.461.8154674.345172.2
1.46-1.522.6205950.798196.60.547
1.52-1.593.1209700.636198.40.39
1.59-1.673.5212110.642199.70.31
1.67-1.783.8213340.71911000.248
1.78-1.913.8213010.84611000.168
1.91-2.113.9213491.06311000.109
2.11-2.413.9213731.40111000.079
2.41-3.043.9213231.90311000.065
3.04-503.9212073.052199.40.049

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.41→9.99 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.713 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The Friedel pairs were used in phasing.
RfactorNum. reflection% reflectionSelection details
Rfree0.207 5140 5 %RANDOM
Rwork0.182 ---
obs0.183 102645 94.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.288 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.41→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4254 0 22 489 4765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224430
X-RAY DIFFRACTIONr_angle_refined_deg1.511.9716001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81925.535215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90615808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2651518
X-RAY DIFFRACTIONr_chiral_restr0.110.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213326
X-RAY DIFFRACTIONr_mcbond_it1.3471.52706
X-RAY DIFFRACTIONr_mcangle_it3.736204405
X-RAY DIFFRACTIONr_scbond_it6.33201724
X-RAY DIFFRACTIONr_scangle_it4.8344.51596
LS refinement shellResolution: 1.41→1.446 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.573 200 -
Rwork0.524 3855 -
all-4055 -
obs--51.6 %
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)
10.2299-0.06110.08830.11990.02750.1959-0.01090.0215-0.01310.01510.00140.01320.008800.0095-0.0067-0.00240.0038-0.0118-0.0021-0.007426.392229.46094.7689
20.34040.0274-0.05570.12490.04510.1278-0.0099-0.02060.0034-0.02430.00180.004-0.0181-0.00980.008-0.00330.0015-0.0021-0.0113-0.001-0.012220.050341.92329.0128
30.0436-0.02820.01760.0182-0.01140.00710.03840.0540.00050.0089-0.0562-0.01850.0152-0.22870.01780.0023-0.0030.00080.0096-0.00910.002720.867735.688516.2578
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A60 - 325
2X-RAY DIFFRACTION2B60 - 325
3X-RAY DIFFRACTION3A401 - 402
4X-RAY DIFFRACTION3B401 - 402

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