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- PDB-3tc7: Crystal Structure of Engineered Protein. Northeast Structural Gen... -

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Basic information

Entry
Database: PDB / ID: 3tc7
TitleCrystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR62.
ComponentsIndole-3-glycerol phosphate synthase
KeywordsLYASE / Engineered Protein / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / OR62 / PSI-Biology
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
ACETIC ACID / PHOSPHATE ION / Indole-3-glycerol phosphate synthase
Similarity search - Component
Biological speciesSulfolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsVorobiev, S. / Su, M. / Bjelic, S. / Kipnis, Y. / Wang, L. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Baker, D. ...Vorobiev, S. / Su, M. / Bjelic, S. / Kipnis, Y. / Wang, L. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Baker, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Exploration of alternate catalytic mechanisms and optimization strategies for retroaldolase design.
Authors: Bjelic, S. / Kipnis, Y. / Wang, L. / Pianowski, Z. / Vorobiev, S. / Su, M. / Seetharaman, J. / Xiao, R. / Kornhaber, G. / Hunt, J.F. / Tong, L. / Hilvert, D. / Baker, D.
History
DepositionAug 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Jan 8, 2014Group: Database references
Revision 1.3Sep 13, 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 / 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 / _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

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Assembly

Deposited unit
A: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1425
Polymers29,7971
Non-polymers3454
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.960, 60.960, 118.663
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Detailsmonomer,31.74 kD,97.9%

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Components

#1: Protein Indole-3-glycerol phosphate synthase / IGPS


Mass: 29797.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: trpC, SSO0895 / Plasmid: pET29b+, OR62-29.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)GOLD
References: UniProt: Q06121, indole-3-glycerol-phosphate synthase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 277 K / Method: microbatch crystallization under oil / pH: 5
Details: 40 % PEG 400, 0.1 M Ammonium phosphate monobasic, 0.1 M Sodium acetate, pH 5.0, Microbatch crystallization under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97915 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 9, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 41749 / Num. obs: 41081 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 14.18 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 29.3
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4119 / % possible all: 92.5

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IGS

1igs


Resolution: 1.5→39.44 Å / Occupancy max: 1 / Occupancy min: 0.41 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2075 5.05 %RANDOM
Rwork0.158 ---
obs0.16 41049 98.46 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.259 Å2 / ksol: 0.416 e/Å3
Displacement parametersBiso max: 45.22 Å2 / Biso mean: 15.707 Å2 / Biso min: 6.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.627 Å2-0 Å2-0 Å2
2--0.627 Å2-0 Å2
3----1.254 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2015 0 19 180 2214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062066
X-RAY DIFFRACTIONf_angle_d1.0922786
X-RAY DIFFRACTIONf_chiral_restr0.072314
X-RAY DIFFRACTIONf_plane_restr0.005357
X-RAY DIFFRACTIONf_dihedral_angle_d14.152801
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.5350.2981350.2332383251891
1.535-1.5730.2511370.2012443258094
1.573-1.6160.2361460.1692487263397
1.616-1.6630.2341230.1572574269798
1.663-1.7170.1891590.1362544270399
1.717-1.7780.1761370.1322598273599
1.778-1.850.1971310.12826522783100
1.85-1.9340.1691320.12125782710100
1.934-2.0360.1651310.1326632794100
2.036-2.1630.1751530.13225792732100
2.163-2.330.1751430.14526482791100
2.33-2.5650.211380.15326502788100
2.565-2.9360.1631300.17126832813100
2.936-3.6980.1911270.17327022829100
3.698-39.4540.2031530.1762790294399

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