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- PDB-1b7e: TRANSPOSASE INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1b7e
TitleTRANSPOSASE INHIBITOR
ComponentsPROTEIN (TRANSPOSASE INHIBITOR PROTEIN FROM TN5)
KeywordsTRANSFERASE INHIBITOR / TRANSPOSASE / POLYNUCLEOTIDYL TRANSFERASE / HYDROLASE
Function / homology
Function and homology information


transposase activity / DNA transposition / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding
Similarity search - Function
Transferase Inhibitor Protein From Tn5; Chain A, domain2 / Transferase Inhibitor Protein From Tn5; Chain / Transposase Inhibitor Protein From Tn5; Chain A, domain 1 / Transposase Inhibitor Protein From Tn5; Chain A, domain 1 / Transposase, IS4-like / Transposase, Tn5-like, N-terminal / Transposase, Tn5-like, C-terminal / Transposase, Tn5-like, N-terminal domain superfamily / : / Transposase DDE domain ...Transferase Inhibitor Protein From Tn5; Chain A, domain2 / Transferase Inhibitor Protein From Tn5; Chain / Transposase Inhibitor Protein From Tn5; Chain A, domain 1 / Transposase Inhibitor Protein From Tn5; Chain A, domain 1 / Transposase, IS4-like / Transposase, Tn5-like, N-terminal / Transposase, Tn5-like, C-terminal / Transposase, Tn5-like, N-terminal domain superfamily / : / Transposase DDE domain / Transposase DNA-binding / Ribonuclease H-like superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2,2':6',2''-TERPYRIDINE PLATINUM(II) Chloride / : / Transposase for transposon Tn5
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsDavies, D.R. / Braam, L.M. / Reznikoff, W.S. / Rayment, I.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: The three-dimensional structure of a Tn5 transposase-related protein determined to 2.9A resolution.
Authors: Davies, D.R. / Braam, L.M. / Reznikoff, W.S. / Rayment, I.
History
DepositionJan 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (TRANSPOSASE INHIBITOR PROTEIN FROM TN5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5033
Polymers47,5761
Non-polymers9282
Water1,00956
1
A: PROTEIN (TRANSPOSASE INHIBITOR PROTEIN FROM TN5)
hetero molecules

A: PROTEIN (TRANSPOSASE INHIBITOR PROTEIN FROM TN5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0066
Polymers95,1512
Non-polymers1,8554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)181.800, 71.900, 41.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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Components

#1: Protein PROTEIN (TRANSPOSASE INHIBITOR PROTEIN FROM TN5)


Mass: 47575.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 622948, UniProt: Q46731*PLUS
#2: Chemical ChemComp-TPT / 2,2':6',2''-TERPYRIDINE PLATINUM(II) Chloride


Mass: 463.799 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H11ClN3Pt
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FOLLOWING RESIDUES WERE DISORDERED BEYOND THE BETA-CARBON AND THUS WERE MODELED AS ALANINE: ...THE FOLLOWING RESIDUES WERE DISORDERED BEYOND THE BETA-CARBON AND THUS WERE MODELED AS ALANINE: GLU72, GLU88, ASP133, ARG215, LYS216, LYS244, VAL246, GLN341, ARG342, MET343, PRO346, ASP347, ASN348, MET352, ASP400, AND GLU 417 ALA 94 WAS DISORDERED BEYOND THE ALPHA-CARBON AND WAS MODELED AS GLYCINE.

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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: 2.84 Å3/Da / Density % sol: 57 % / Description: STRUCTURE WAS INDEPENDENTLY SOLVED USING MIR
Crystal growpH: 6 / Details: pH 6.0
Crystal
*PLUS
Density % sol: 57 %
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 mg/mlprotein11
220 %PEG800011
3100 mMtetraethylammonium sulfate11
4100 mMMES11

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0273,1.0720,1.1201
DetectorType: BRUKER / Detector: CCD / Details: MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.02731
21.0721
31.12011
ReflectionResolution: 2.9→30 Å / Num. all: 13121 / Num. obs: 13121 / % possible obs: 94.3 % / Redundancy: 2.98 % / Rsym value: 0.05 / Net I/σ(I): 30.9
Reflection shellResolution: 2.9→3 Å / Mean I/σ(I) obs: 7.5 / Rsym value: 0.204 / % possible all: 87
Reflection
*PLUS
Num. measured all: 69105 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 87 % / Rmerge(I) obs: 0.204

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Processing

Software
NameVersionClassification
DENZO2000data reduction
SCALEPACK2000data scaling
SOLVEphasing
TNTrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.9→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.195 --
all-12174 -
obs-12174 94.3 %
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2887 0 38 56 2981
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_deg2.63
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.009
X-RAY DIFFRACTIONt_gen_planes0.01
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_planar_d0.009
X-RAY DIFFRACTIONt_plane_restr0.01

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