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- PDB-3k4h: CRYSTAL STRUCTURE OF putative transcriptional regulator LacI from... -

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Basic information

Entry
Database: PDB / ID: 3k4h
TitleCRYSTAL STRUCTURE OF putative transcriptional regulator LacI from Bacillus cereus subsp. cytotoxis NVH 391-98
Componentsputative transcriptional regulatorTranscriptional regulation
Keywordstranscription regulator / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / DNA-binding / Transcription / Transcription regulation / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homologyPeriplasmic binding protein-like domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / alpha-maltose / Putative transcriptional regulator
Function and homology information
Biological speciesBacillus cytotoxicus NVH 391-98 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsMalashkevich, V.N. / Toro, R. / Morano, C. / 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 putative transcriptional regulator LacI from Bacillus cereus subsp. cytotoxis NVH 391-98
Authors: Malashkevich, V.N. / Toro, R. / Morano, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionOct 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 24, 2012Group: Structure summary
Revision 1.3Nov 1, 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 1.4Nov 21, 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 / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 10, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9654
Polymers65,2802
Non-polymers6852
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-2 kcal/mol
Surface area24520 Å2
MethodPISA
2
A: putative transcriptional regulator
hetero molecules

B: putative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9654
Polymers65,2802
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z+1/41
Buried area4150 Å2
ΔGint-13 kcal/mol
Surface area23200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.607, 98.607, 186.749
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A-99999 - 99999
2111B-99999 - 99999
Detailsauthors state that the biological unit is the same as asymmetric unit.

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Components

#1: Protein putative transcriptional regulator / Transcriptional regulation


Mass: 32640.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cytotoxicus NVH 391-98 (bacteria)
Strain: cytotoxis NVH 391-98 / Gene: Bcer98_2711, Q2E7G6 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: D0VWZ8*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.48 Å3/Da / Density % sol: 64.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG8000, 0.1M MES, 0.2M Ca(OAc)2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 48261 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 8
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 4.9 % / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0089refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 21.107 / SU ML: 0.181 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The maltose binding is only suggested based a) on the shape of electron density, b) the fact that other members of this group of proteins ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The maltose binding is only suggested based a) on the shape of electron density, b) the fact that other members of this group of proteins bind maltose or lactose, c) suggested inhibitor makes multiple favorable contacts in the binding site. Lactose does not fit the density, but we can not exclude that some other similar sugar is bound. PLEASE REMOVE "complexed with maltose" from the title, and just add remark that maltose binding is SUGGESTED.
RfactorNum. reflection% reflectionSelection details
Rfree0.24388 1191 5.1 %RANDOM
Rwork0.20297 ---
obs0.20503 22103 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.824 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2---0.77 Å20 Å2
3---1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4347 0 46 24 4417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224477
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9866062
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2715558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57424.922193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.30115779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8161520
X-RAY DIFFRACTIONr_chiral_restr0.0960.2710
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213296
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0733.52781
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.825504490
X-RAY DIFFRACTIONr_scbond_it11.287501694
X-RAY DIFFRACTIONr_scangle_it0.9684.51572
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2165 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.925
tight thermal8.8610
LS refinement shellResolution: 2.798→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 92 -
Rwork0.239 1501 -
obs--96.25 %
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)
12.07240.8480.12262.0199-0.04491.0338-0.01710.2599-0.0916-0.01940.1054-0.12580.00530.0385-0.08830.0182-0.00070.01790.0333-0.01320.042867.598813.2441107.6666
24.14470.6760.65542.16060.56691.79270.19060.18950.1803-0.08940.0503-0.1159-0.21730.2695-0.2410.0763-0.01950.05240.056-0.03750.062369.68075.865277.6464
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 288
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION1A503 - 529
4X-RAY DIFFRACTION2B5 - 282
5X-RAY DIFFRACTION2B501
6X-RAY DIFFRACTION2B503 - 513

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