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- PDB-4ix0: Computational Design of an Unnatural Amino Acid Metalloprotein wi... -

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Basic information

Entry
Database: PDB / ID: 4ix0
TitleComputational Design of an Unnatural Amino Acid Metalloprotein with Atomic Level Accuracy
ComponentsUnnatural Amino Acid Mediated Metalloprotein
KeywordsMETAL BINDING PROTEIN / computational design / TIM barrel / metalloprotein / bipyridylalanine
Function / homology
Function and homology information


indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / tryptophan biosynthetic process
Similarity search - Function
Indole-3-glycerol phosphate synthase, conserved site / Indole-3-glycerol phosphate synthase signature. / Indole-3-glycerol phosphate synthase domain / Indole-3-glycerol phosphate synthase / Indole-3-glycerol phosphate synthase / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Indole-3-glycerol phosphate synthase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMills, J. / Bolduc, J. / Khare, S. / Stoddard, B. / Baker, D.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Computational design of an unnatural amino Acid dependent metalloprotein with atomic level accuracy.
Authors: Mills, J.H. / Khare, S.D. / Bolduc, J.M. / Forouhar, F. / Mulligan, V.K. / Lew, S. / Seetharaman, J. / Tong, L. / Stoddard, B.L. / Baker, D.
History
DepositionJan 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Unnatural Amino Acid Mediated Metalloprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0254
Polymers29,7741
Non-polymers2513
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.573, 62.790, 92.709
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Unnatural Amino Acid Mediated Metalloprotein / Indole-3-glycerol phosphate synthase / IGPS


Mass: 29774.086 Da / Num. of mol.: 1
Mutation: K10E, F22V, S70A, K110M, I133BPA, N161T, N179T, R181Q, L183D, E209D, F246L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: trpC, SSO0895 / Plasmid: pet28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q06121
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5
Details: 1.6 M ammonium sulfate, 3% PEG3350, pH 6.5, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 31, 2012 / Details: Varimax HR
RadiationMonochromator: Varimax HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→51.99 Å / Num. all: 11274 / Num. obs: 10998 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 37.86 Å2 / Rsym value: 0.083 / Net I/σ(I): 9.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.3 % / Num. unique all: 1037 / Rsym value: 0.39 / % possible all: 95.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→51.99 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.907 / SU B: 9.845 / SU ML: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.498 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25699 526 4.8 %RANDOM
Rwork0.20035 ---
all0.2031 10396 --
obs0.2031 10396 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.488 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å2-0 Å2
2--0.26 Å2-0 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.5→51.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 11 39 2038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222037
X-RAY DIFFRACTIONr_angle_refined_deg2.0812.0112749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5235250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.06923.97893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.20615398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3451520
X-RAY DIFFRACTIONr_chiral_restr0.1320.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211495
X-RAY DIFFRACTIONr_mcbond_it1.0661.51239
X-RAY DIFFRACTIONr_mcangle_it2.08322013
X-RAY DIFFRACTIONr_scbond_it3.3023798
X-RAY DIFFRACTIONr_scangle_it5.5344.5734
LS refinement shellResolution: 2.5→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 39 -
Rwork0.331 691 -
obs-691 91.02 %

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