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Basic information

Entry
Database: PDB / ID: 4iww
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 / Indole-3-glycerol phosphate synthase, conserved site / Indole-3-glycerol phosphate synthase signature. / Indole-3-glycerol phosphate synthase domain / 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
: / Indole-3-glycerol phosphate synthase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 4, 2013Group: Derived calculations
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3Sep 20, 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_ncs_dom_lim / 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_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_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_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
B: Unnatural Amino Acid Mediated Metalloprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,53113
Polymers59,5482
Non-polymers98211
Water1,22568
1
A: Unnatural Amino Acid Mediated Metalloprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4098
Polymers29,7741
Non-polymers6357
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Unnatural Amino Acid Mediated Metalloprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1215
Polymers29,7741
Non-polymers3474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.265, 60.265, 123.566
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 2 - 248 / Label seq-ID: 1 - 247

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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.: 2
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5
Details: 1.8 M ammonium sulfate, 5% 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: Jun 26, 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: 2.3→123.6 Å / Num. all: 22369 / Num. obs: 20826 / % possible obs: 93.1 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 20.86 Å2 / Rsym value: 0.041 / Net I/σ(I): 24.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.3 % / Num. unique all: 2195 / Rsym value: 0.079 / % possible all: 96.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASER(CCP4)phasing
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IGS

1igs


Resolution: 2.3→123.57 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.89 / SU B: 7.033 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.555 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2636 1068 5.1 %RANDOM
Rwork0.2087 ---
all0.21164 19758 --
obs0.21164 19758 93.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.841 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å2-0 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.3→123.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3988 0 47 68 4103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224080
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4552.0175501
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2815492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.07423.946185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.35315796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3461540
X-RAY DIFFRACTIONr_chiral_restr0.1010.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212970
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6451.52466
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22624005
X-RAY DIFFRACTIONr_scbond_it2.0331614
X-RAY DIFFRACTIONr_scangle_it3.3854.51496
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
988medium positional0.060.5
1005loose positional0.355
988medium thermal0.52
1005loose thermal0.9110
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 79 -
Rwork0.184 --
obs-1530 96.93 %

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