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- PDB-5vht: E. coli chorismate mutase with orthogonal interface containing p-... -

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Basic information

Entry
Database: PDB / ID: 5vht
TitleE. coli chorismate mutase with orthogonal interface containing p-benzoyl phenylalanine
ComponentsChorismate Mutase
KeywordsISOMERASE / p-benzoyl phenylalanine / orthogonal interface / chorismate mutase / mutagenesis
Function / homology
Function and homology information


arogenate dehydratase activity / prephenate dehydratase / prephenate dehydratase activity / tyrosine biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / L-phenylalanine biosynthetic process / protein homodimerization activity / cytoplasm
Similarity search - Function
Chorismate mutase, gammaproteobacteria / Prephenate dehydratase signature 1. / Prephenate dehydratase signature 2. / Bifunctional P-protein, chorismate mutase/prephenate dehydratase / Prephenate dehydratase, conserved site / Prephenate dehydratase / Prephenate dehydratase / Prephenate dehydratase domain profile. / Chorismate mutase / Chorismate Mutase Domain, subunit A ...Chorismate mutase, gammaproteobacteria / Prephenate dehydratase signature 1. / Prephenate dehydratase signature 2. / Bifunctional P-protein, chorismate mutase/prephenate dehydratase / Prephenate dehydratase, conserved site / Prephenate dehydratase / Prephenate dehydratase / Prephenate dehydratase domain profile. / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / ACT domain profile. / ACT domain / ACT-like domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bifunctional chorismate mutase/prephenate dehydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKoh, M. / Nasertorabi, F. / Han, G.W. / Stevens, R.C. / Shultz, P.G.
Funding support United States, Korea, Republic Of, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0011787 United States
Korean Ministry of EducationNRF- 210 2016R1A6A3A03009203 Korea, Republic Of
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Generation of an Orthogonal Protein-Protein Interface with a Noncanonical Amino Acid.
Authors: Koh, M. / Nasertorabi, F. / Han, G.W. / Stevens, R.C. / Schultz, P.G.
History
DepositionApr 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chorismate Mutase
B: Chorismate Mutase


Theoretical massNumber of molelcules
Total (without water)23,2732
Polymers23,2732
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-50 kcal/mol
Surface area10910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.861, 61.270, 62.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 4 - 98 / Label seq-ID: 4 - 98

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

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Components

#1: Protein Chorismate Mutase / CM


Mass: 11636.413 Da / Num. of mol.: 2 / Fragment: UNP residues 1-92 / Mutation: L25F, Y72PBF, L76T, I80G, D83Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: pheA, b2599, JW2580 / Plasmid: PET 22+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P0A9J8, chorismate mutase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1.92 Å3/Da / Density % sol: 35.96 % / Description: rectangular
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100mM Bicine pH9.0, 100mM Na-Acetate and 32% PEG 8K
PH range: 7.5-9.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryo
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2→23.75 Å / Num. obs: 12193 / % possible obs: 99.7 % / Redundancy: 8.3 % / Biso Wilson estimate: 31.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.065 / Net I/σ(I): 8.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1735 / CC1/2: 0.73 / Rpim(I) all: 0.431 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSv. Nov 1 2016data scaling
SCALA3.3.22data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ECM

1ecm


Resolution: 2→23.73 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.595 / SU ML: 0.155 / Cross valid method: FREE R-VALUE / ESU R: 0.245 / ESU R Free: 0.183 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24017 593 4.9 %RANDOM
Rwork0.21336 ---
obs0.21475 11535 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.85 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å20 Å20 Å2
2--0.03 Å20 Å2
3---1.97 Å2
Refinement stepCycle: 1 / Resolution: 2→23.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1494 0 0 73 1567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191571
X-RAY DIFFRACTIONr_bond_other_d0.0010.021538
X-RAY DIFFRACTIONr_angle_refined_deg1.44522131
X-RAY DIFFRACTIONr_angle_other_deg0.95933520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7825200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.34221.2962
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23715281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7241517
X-RAY DIFFRACTIONr_chiral_restr0.0870.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02337
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_it3.1214.182782
X-RAY DIFFRACTIONr_mcbond_other3.1144.178781
X-RAY DIFFRACTIONr_mcangle_it4.5266.235982
X-RAY DIFFRACTIONr_mcangle_other4.5246.239983
X-RAY DIFFRACTIONr_scbond_it3.9394.72789
X-RAY DIFFRACTIONr_scbond_other3.9364.722790
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1876.9061147
X-RAY DIFFRACTIONr_long_range_B_refined8.30250.3191746
X-RAY DIFFRACTIONr_long_range_B_other8.29750.1951735
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5498 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 37 -
Rwork0.297 824 -
obs--96.96 %

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