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- PDB-3tsm: Crystal structure of Indole-3-glycerol phosphate synthase from Br... -

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Basic information

Entry
Database: PDB / ID: 3tsm
TitleCrystal structure of Indole-3-glycerol phosphate synthase from Brucella melitensis
ComponentsIndole-3-glycerol phosphate synthase
KeywordsLYASE / synthase / Structural Genomics / SSGCID / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase 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
Unknown ligand / Indole-3-glycerol phosphate synthase
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Indole-3-glycerol phosphate synthase from Brucella melitensis
Authors: Gardberg, A. / Edwards, T. / Sankaran, B. / Staker, B. / Stewart, L.
History
DepositionSep 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,5847
Polymers59,2122
Non-polymers3725
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-40 kcal/mol
Surface area20730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.800, 73.290, 118.940
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 Indole-3-glycerol phosphate synthase / IGPS


Mass: 29605.947 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: 2308 / Gene: trpC, BAB1_1164 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2YRR4, indole-3-glycerol-phosphate synthase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Internal tracking number 223543D9. Crystallant (JCSG D9): 25.5% PEG 4000, 15% glycerol, 170 mM Ammonium Sulfate. Protein: BrabA.17351.a.A1 PS01096 at 63 mg/ml in a buffer consisting of 25 mM ...Details: Internal tracking number 223543D9. Crystallant (JCSG D9): 25.5% PEG 4000, 15% glycerol, 170 mM Ammonium Sulfate. Protein: BrabA.17351.a.A1 PS01096 at 63 mg/ml in a buffer consisting of 25 mM HEPES, 300-500 mM NaCl, 2 mM DTT, 0.025% sodium azide, 5% glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 9, 2011
RadiationMonochromator: Asymmetric curved crystal, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 34823 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 30.856 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 13.57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.15-2.217.40.4694.2188122537100
2.21-2.270.454.717408244399.3
2.27-2.330.4044.917922242699.4
2.33-2.40.3156.2173182331100
2.4-2.480.2876.8167682263100
2.48-2.570.2328.1164632217100
2.57-2.670.2089155812104100
2.67-2.780.1810.6152062072100
2.78-2.90.15311.914466195599.9
2.9-3.040.12314.1139551890100
3.04-3.210.09917.1133671810100
3.21-3.40.08719.1124721700100
3.4-3.630.07322.6115111599100
3.63-3.930.0682510581149999.8
3.93-4.30.06126.599981394100
4.3-4.810.05727.590551272100
4.81-5.550.0626.478701130100
5.55-6.80.0625.46788959100
6.8-9.620.0529.85371770100
9.620.04730.3287345299.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.1 Å
Translation2.5 Å47.1 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: molecular replacement
Starting model: PDB entry 1pii

1pii


Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 8.276 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1751 5 %RANDOM
Rwork0.183 ---
obs0.185 34822 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.438 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2---1.14 Å20 Å2
3---1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3905 0 28 248 4181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194035
X-RAY DIFFRACTIONr_bond_other_d0.0040.022781
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9945458
X-RAY DIFFRACTIONr_angle_other_deg1.16636774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1955533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01923.509171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06815695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0751537
X-RAY DIFFRACTIONr_chiral_restr0.080.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214542
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02815
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 97 -
Rwork0.205 2241 -
all-2338 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
111.97251.2332.52021.20740.34573.1728-0.0799-0.42460.439-0.1126-0.08360.1384-0.2131-0.21480.16340.03810.00530.00320.0337-0.05050.1026-25.4845-4.460417.2586
21.37851.08690.37042.00870.36560.3339-0.1070.1464-0.0755-0.10830.1246-0.1448-0.01130.0458-0.01760.0254-0.023-0.00070.0279-0.01140.05225.81398.623116.0592
33.80341.2016-1.3294.3499-1.533.62380.03360.21760.3239-0.0305-0.01220.432-0.0564-0.0886-0.02140.03670.004-0.04440.0307-0.00960.1344-0.438124.998622.1562
41.9394-0.1174-1.37942.18981.43343.6764-0.19560.25570.0583-0.30530.1466-0.1124-0.2632-0.05240.0490.0987-0.0643-0.01340.060.00820.084213.252525.573515.8393
52.25053.15891.135218.7245-0.31753.284-0.46380.20310.2737-0.46380.23160.3415-0.2318-0.08550.23220.104-0.0487-0.07720.03680.03240.1122-10.3497.575810.3707
61.71680.76550.48110.78240.13220.56710.1102-0.1106-0.1350.0563-0.0446-0.09440.0393-0.035-0.06560.0256-0.0178-0.01230.01480.00670.0237-26.9068-21.156414.773
75.69490.0762-1.89462.74060.43243.1313-0.039-0.14730.26250.1570.06480.0566-0.0891-0.043-0.02580.05550.002-0.02890.0116-0.0020.0334-41.3421-15.14786.0147
81.67020.03661.05320.7715-0.66654.18090.1966-0.2638-0.11250.0701-0.13390.1143-0.0017-0.1924-0.06270.0467-0.0524-0.0060.0826-0.00260.0418-44.4696-27.112613.0366
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 23
2X-RAY DIFFRACTION2A24 - 172
3X-RAY DIFFRACTION3A173 - 205
4X-RAY DIFFRACTION4A206 - 264
5X-RAY DIFFRACTION5B5 - 23
6X-RAY DIFFRACTION6B24 - 172
7X-RAY DIFFRACTION7B173 - 205
8X-RAY DIFFRACTION8B206 - 264

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