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- PDB-2hxx: Aminotryptophan Barstar -

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Basic information

Entry
Database: PDB / ID: 2hxx
TitleAminotryptophan Barstar
ComponentsBarstar
KeywordsHYDROLASE INHIBITOR / Aminotryptophan / Barstar / Genetic code / Protein folding / Stability
Function / homologyBarstar-like / Barstar (barnase inhibitor) / Barstar (barnase inhibitor) / Barstar-like superfamily / Barnase; Chain D / 2-Layer Sandwich / cytoplasm / Alpha Beta / Barstar
Function and homology information
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRubini, M. / Lepthien, S. / Golbik, R. / Budisa, N.
CitationJournal: BIOCHIM.BIOPHYS.ACTA / Year: 2006
Title: Aminotryptophan-containing barstar
Authors: Rubini, M. / Lepthien, S. / Golbik, R. / Budisa, N.
History
DepositionAug 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2012Group: Structure summary
Revision 1.4Oct 18, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _software.name
Revision 1.5Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Barstar
B: Barstar


Theoretical massNumber of molelcules
Total (without water)20,3532
Polymers20,3532
Non-polymers00
Water1,26170
1
A: Barstar


Theoretical massNumber of molelcules
Total (without water)10,1761
Polymers10,1761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Barstar


Theoretical massNumber of molelcules
Total (without water)10,1761
Polymers10,1761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.160, 46.850, 51.060
Angle α, β, γ (deg.)90.00, 121.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Barstar / Ribonuclease inhibitor


Mass: 10176.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Plasmid: pQE30-b* / Production host: Escherichia coli (E. coli) / Strain (production host): ATCC49980 / References: UniProt: P11540
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.4 M Ammonium sulfate, 50 mM Tris/Hcl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 19, 2004 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.97→20 Å / Num. all: 32530 / Num. obs: 11770 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.048 / Net I/σ(I): 19.01
Reflection shellResolution: 1.97→2 Å / % possible all: 88.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345345DTBdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→17.14 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1181841.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 564 5.1 %RANDOM
Rwork0.251 ---
obs0.251 11128 94.8 %-
all-11768 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.9412 Å2 / ksol: 0.322794 e/Å3
Displacement parametersBiso mean: 36.9 Å2
Baniso -1Baniso -2Baniso -3
1--11.6 Å20 Å2-5.11 Å2
2---7.01 Å20 Å2
3---18.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2→17.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1438 0 0 70 1508
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it2.121.5
X-RAY DIFFRACTIONc_mcangle_it3.232
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.132.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.425 80 4.5 %
Rwork0.399 1706 -
obs-1706 91.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4trn_mod.partrn.top

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