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- PDB-3lcz: B.licheniformis Anti-TRAP can assemble into two types of dodecame... -

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Basic information

Entry
Database: PDB / ID: 3lcz
TitleB.licheniformis Anti-TRAP can assemble into two types of dodecameric particles with the same symmetry but inverted orientation of trimers
ComponentsInhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
KeywordsGENE REGULATION / Anti-TRAP / AT / TRAP / tryptophan RNA-binding attenuation protein / transcription attenuation / antitermination / transcription factors / tryptophan biosynthesis regulation
Function / homologyChaperone, DNAj Protein; Chain A / Chaperone, DNAj Protein; Chain A - #10 / Tryptophan RNA-binding attenuator protein inhibitory protein / Tryptophan RNA-binding attenuator protein inhibitory protein / Heat shock protein DnaJ, cysteine-rich domain superfamily / Other non-globular / Special / metal ion binding / Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
Function and homology information
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsShevtsov, M.B. / Chen, Y. / Gollnick, P. / Antson, A.A.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Bacillus licheniformis Anti-TRAP can assemble into two types of dodecameric particles with the same symmetry but inverted orientation of trimers.
Authors: Shevtsov, M.B. / Chen, Y. / Isupov, M.N. / Leech, A. / Gollnick, P. / Antson, A.A.
History
DepositionJan 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
B: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
C: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
D: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2288
Polymers22,9664
Non-polymers2624
Water2,036113
1
A: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
B: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
C: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
D: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
hetero molecules

A: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
B: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
C: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
D: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
hetero molecules

A: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
B: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
C: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
D: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,68424
Polymers68,89912
Non-polymers78512
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area23660 Å2
ΔGint-174 kcal/mol
Surface area28210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.076, 108.076, 49.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA / YczA


Mass: 5741.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Strain: 5A32 / Gene: BL05022, BLi00308, rtpA, rtpA (YczA), yczA / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta BL21(DE3) competent cells / References: UniProt: Q65NU7
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Bis-Tris buffer pH 5.5-6.0 and 23-27 % of poly(ethylene) glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.28 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 2.06→54 Å / Num. all: 13298 / Num. obs: 13005 / % possible obs: 97.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 46.7 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.2
Reflection shellResolution: 2.06→2.13 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1265 / % possible all: 95.1

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.3.0008refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2bx9

2bx9


Resolution: 2.06→28.76 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.916 / SU B: 13.741 / SU ML: 0.189 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28578 647 5 %RANDOM
Rwork0.21309 ---
all0.21661 ---
obs0.21661 12301 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.009 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.226 Å0.254 Å
Refinement stepCycle: LAST / Resolution: 2.06→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 4 113 1709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221651
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.791.9982228
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.945208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.84226.30865
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49315297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.677154
X-RAY DIFFRACTIONr_chiral_restr0.1470.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021212
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.30.2861
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3270.21159
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2890.2113
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5971.51085
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.54221721
X-RAY DIFFRACTIONr_scbond_it6.1013602
X-RAY DIFFRACTIONr_scangle_it7.584.5507
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.062→2.116 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 46 -
Rwork0.253 879 -
obs-925 94.97 %
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)
17.36140.87292.85584.96142.0587.78540.1564-0.296-0.15350.34190.0088-0.5899-0.3042-0.0513-0.1652-0.17380.06610.111-0.28930.1883-0.125514.702153.2536-5.0297
29.8395-9.2118-1.74799.03531.76470.35060.17150.3598-0.4802-0.3434-0.0061-0.0905-0.1040.0086-0.1654-0.15760.07890.2379-0.1291-0.0020.031718.935340.171-18.969
39.7015-2.8626-4.35936.10263.44367.22530.0038-0.40410.05390.4517-0.136-0.41430.05520.04940.1322-0.1752-0.01260.0642-0.25180.2341-0.08399.082148.6509-0.6028
44.1207-2.50915.664610.1113-7.518811.75640.3578-0.49-0.29861.4938-0.1428-0.4960.4233-0.3045-0.2150.46110.04370.18160.05840.19340.08121.692540.346815.2369
55.3748-0.6244-0.445615.9451-0.66589.2023-0.0618-0.5626-0.35290.3366-0.2993-0.8923-0.317-0.00620.3611-0.14420.02960.0248-0.11430.1808-0.193213.085355.3372.8693
62.7968-1.5976-3.94370.91262.25275.5609-0.2639-0.59510.6928-0.98380.6117-0.5711-0.10561.2782-0.34790.4932-0.1615-0.1360.23160.20630.831127.287166.97376.4076
711.13790.2383.35088.0469-1.6224.4262-0.40320.3091-0.1135-0.1413-0.0777-0.1854-0.1931-0.30930.4809-0.15360.03070.0812-0.1857-0.0614-0.38751.744757.912-24.0793
85.6393-3.738-6.56533.33952.621111.1194-0.42731.0341-0.1216-0.2214-0.26650.50410.51080.02820.6938-0.1065-0.01190.11330.22960.057-0.031520.601751.6127-29.3742
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 9
2X-RAY DIFFRACTION1A36 - 53
3X-RAY DIFFRACTION2A10 - 35
4X-RAY DIFFRACTION3B1 - 9
5X-RAY DIFFRACTION3B36 - 53
6X-RAY DIFFRACTION4B10 - 35
7X-RAY DIFFRACTION5C1 - 9
8X-RAY DIFFRACTION5C36 - 53
9X-RAY DIFFRACTION6C10 - 35
10X-RAY DIFFRACTION7D1 - 9
11X-RAY DIFFRACTION7D36 - 53
12X-RAY DIFFRACTION8D10 - 35

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