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Basic information

Entry
Database: PDB / ID: 4lny
TitleCrystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR422
ComponentsEngineered Protein OR422
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Engineered Protein
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
: / Indole-3-glycerol phosphate synthase
Similarity search - Component
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.929 Å
AuthorsVorobiev, S. / Su, M. / Bjelic, S. / Kipnis, Y. / Wang, L. / Sahdev, S. / Xiao, R. / Maglaqui, M. / Kogan, S. / Baker, D. ...Vorobiev, S. / Su, M. / Bjelic, S. / Kipnis, Y. / Wang, L. / Sahdev, S. / Xiao, R. / Maglaqui, M. / Kogan, S. / Baker, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of Engineered Protein OR422.
Authors: Vorobiev, S. / Su, M. / Bjelic, S. / Kipnis, Y. / Wang, L. / Sahdev, S. / Xiao, R. / Maglaqui, M. / Kogan, S. / Baker, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJul 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 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

Downloads & links

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Assembly

Deposited unit
A: Engineered Protein OR422
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,97512
Polymers30,1241
Non-polymers85211
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.125, 63.161, 86.436
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsmonomer,28.43 kD,98.9%

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Components

#1: Protein Engineered Protein OR422


Mass: 30123.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Plasmid: OR422-29.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q06121*PLUS
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 1.86 Å3/Da / Density % sol: 33.99 %
Crystal growTemperature: 291 K / Method: microbatch crystallization under oil / pH: 4.6
Details: 30% PEG 400, 0.1M cadmium chloride, 0.1M sodium acetate, pH 4.6, Microbatch crystallization under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 6, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.93→43.22 Å / Num. all: 32780 / Num. obs: 32707 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Biso Wilson estimate: 25.84 Å2 / Rmerge(I) obs: 0.176 / Net I/σ(I): 13.5
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.01437 / Mean I/σ(I) obs: 2.3 / Num. unique all: 5451 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
RAPDdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TC7

3tc7


Resolution: 1.929→37.136 Å / Occupancy max: 1 / Occupancy min: 0.48 / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1655 5.06 %RANDOM
Rwork0.191 ---
obs0.192 32699 99.91 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.577 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 138.7 Å2 / Biso mean: 32.227 Å2 / Biso min: 11.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.759 Å2-0 Å20 Å2
2---9.178 Å20 Å2
3---7.419 Å2
Refinement stepCycle: LAST / Resolution: 1.929→37.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1995 0 11 129 2135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062024
X-RAY DIFFRACTIONf_angle_d1.2752728
X-RAY DIFFRACTIONf_chiral_restr0.095310
X-RAY DIFFRACTIONf_plane_restr0.005351
X-RAY DIFFRACTIONf_dihedral_angle_d15.273790
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.929-1.9860.3171440.3132584272899
1.986-2.050.2791480.26725632711100
2.05-2.1240.2731260.23125932719100
2.124-2.2080.2521610.21825722733100
2.208-2.3090.2741350.20625862721100
2.309-2.4310.2411240.19226232747100
2.431-2.5830.2231170.18325952712100
2.583-2.7820.21590.18325572716100
2.782-3.0620.2251410.17425902731100
3.062-3.5050.2171300.17425952725100
3.505-4.4150.1891220.16326152737100
4.415-37.1430.1991480.18725712719100
Refinement TLS params.Method: refined / Origin x: 30.1412 Å / Origin y: 26.2346 Å / Origin z: 24.2183 Å
111213212223313233
T0.061 Å20.0005 Å20.0065 Å2-0.0687 Å20.0034 Å2--0.0628 Å2
L0.2129 °20.3875 °2-0.0953 °2-0.7978 °20.1716 °2--0.6468 °2
S-0.0284 Å °0.0195 Å °-0.0031 Å °0.0402 Å °0.0225 Å °0.0515 Å °0.061 Å °0.0217 Å °-0 Å °
Refinement TLS groupSelection details: chain A

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