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- PDB-1am2: GYRA INTEIN FROM MYCOBACTERIUM XENOPI -

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Basic information

Entry
Database: PDB / ID: 1am2
TitleGYRA INTEIN FROM MYCOBACTERIUM XENOPI
ComponentsMXE GYRA INTEIN
KeywordsINTEIN / PROTEIN SPLICING
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / intein-mediated protein splicing / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Topoisomerase (Topo) IIA-type catalytic domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A ...Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Topoisomerase (Topo) IIA-type catalytic domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / DNA topoisomerase, type IIA-like domain superfamily / Beta Complex / Mainly Beta
Similarity search - Domain/homology
DNA gyrase subunit A
Similarity search - Component
Biological speciesMycobacterium xenopi (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsKlabunde, T. / Sharma, S. / Sacchettini, J.C.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Crystal structure of GyrA intein from Mycobacterium xenopi reveals structural basis of protein splicing.
Authors: Klabunde, T. / Sharma, S. / Telenti, A. / Jacobs Jr., W.R. / Sacchettini, J.C.
History
DepositionJun 20, 1997Processing site: BNL
Revision 1.0Jun 24, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MXE GYRA INTEIN


Theoretical massNumber of molelcules
Total (without water)21,3641
Polymers21,3641
Non-polymers00
Water82946
1
A: MXE GYRA INTEIN

A: MXE GYRA INTEIN


Theoretical massNumber of molelcules
Total (without water)42,7282
Polymers42,7282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Unit cell
Length a, b, c (Å)55.700, 55.700, 133.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein MXE GYRA INTEIN


Mass: 21364.070 Da / Num. of mol.: 1 / Mutation: Y0A, C1S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium xenopi (bacteria) / Gene: RTP / Gene (production host): RTP / Production host: Escherichia coli (E. coli) / References: UniProt: P72065
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.77 Å3/Da / Density % sol: 56 %
Crystal growpH: 5.5 / Details: pH 5.5
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDUnitCommon nameCrystal-IDSol-IDChemical formula
1mg/mlprotein1drop
2mMdithiothreitol1drop
3mMsodium citrate1reservoir
5mMammonium sulfate1reservoir
4mM1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 23, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 14058 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 4.18 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 15.2
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 3.67 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.65 / Rsym value: 0.25 / % possible all: 96.8
Reflection
*PLUS
Num. measured all: 58763
Reflection shell
*PLUS
% possible obs: 96.8 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→8 Å / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.252 -10 %RANDOM
Rwork0.187 ---
obs0.187 11243 90.4 %-
Displacement parametersBiso mean: 31.8 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 0 46 1421
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.462
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.24 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3276 -8.73 %
Rwork0.2625 459 -
obs--84.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.2625

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