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- PDB-6bma: The crystal structure of indole-3-glycerol phosphate synthase fro... -

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Basic information

Entry
Database: PDB / ID: 6bma
TitleThe crystal structure of indole-3-glycerol phosphate synthase from Campylobacter jejuni subsp. jejuni NCTC 11168
ComponentsIndole-3-glycerol phosphate synthase
KeywordsLYASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / L-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
ACETATE ION / FORMIC ACID / : / PHOSPHATE ION / Indole-3-glycerol phosphate synthase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsTan, K. / Zhou, M. / Nocek, B. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: The crystal structure of indole-3-glycerol phosphate synthase from Campylobacter jejuni subsp. jejuni NCTC 11168
Authors: Tan, K. / Zhou, M. / Nocek, B. / Joachimiak, A.
History
DepositionNov 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry
Revision 1.3Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)61,06920
Polymers59,7802
Non-polymers1,28918
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-97 kcal/mol
Surface area20860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.181, 148.181, 149.947
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-301-

K

21A-302-

CL

31B-301-

K

41B-302-

CL

51A-455-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 29890.100 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter)
Strain: ATCC 700819 / NCTC 11168 / Gene: trpC, Cj0498 / Cell (production host): BL21(DE3)magic / Production host: Escherichia coli (E. coli)
References: UniProt: Q9PI11, indole-3-glycerol-phosphate synthase

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Non-polymers , 7 types, 194 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 1.0M NaH2PO4/K2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 23, 2010 / Details: mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.98→41.45 Å / Num. obs: 43974 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 30.34 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.038 / Rrim(I) all: 0.084 / Χ2: 1.832 / Net I/σ(I): 29.3
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2128 / CC1/2: 0.72 / Rpim(I) all: 0.367 / Rrim(I) all: 0.765 / Χ2: 1.279 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TSM

3tsm


Resolution: 1.98→41.435 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6
RfactorNum. reflection% reflectionSelection details
Rfree0.196 2193 4.99 %random
Rwork0.1671 ---
obs0.1685 43947 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.98→41.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4085 0 68 177 4330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064243
X-RAY DIFFRACTIONf_angle_d0.7935715
X-RAY DIFFRACTIONf_dihedral_angle_d17.5832601
X-RAY DIFFRACTIONf_chiral_restr0.052652
X-RAY DIFFRACTIONf_plane_restr0.005720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.02310.28421340.22952562X-RAY DIFFRACTION99
2.0231-2.07010.20821230.19852589X-RAY DIFFRACTION100
2.0701-2.12190.22141390.19412579X-RAY DIFFRACTION100
2.1219-2.17930.24981260.18492586X-RAY DIFFRACTION100
2.1793-2.24340.24261360.18392624X-RAY DIFFRACTION100
2.2434-2.31580.21321320.18592588X-RAY DIFFRACTION100
2.3158-2.39860.23911390.18472585X-RAY DIFFRACTION100
2.3986-2.49460.24051390.17752602X-RAY DIFFRACTION100
2.4946-2.60810.19781400.17662596X-RAY DIFFRACTION100
2.6081-2.74560.23661460.18232620X-RAY DIFFRACTION100
2.7456-2.91750.20941430.18122587X-RAY DIFFRACTION100
2.9175-3.14270.20341480.16992594X-RAY DIFFRACTION100
3.1427-3.45890.17481320.16752630X-RAY DIFFRACTION100
3.4589-3.9590.16761430.14062641X-RAY DIFFRACTION100
3.959-4.98660.14981420.1332639X-RAY DIFFRACTION100
4.9866-41.44430.19431310.17262732X-RAY DIFFRACTION99
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)
13.0173-0.23121.08516.48470.16498.6213-0.1058-1.0858-0.81720.61960.1108-0.30870.8495-0.263-0.10090.3708-0.0375-0.01410.41220.08270.3759-21.2831-24.726-8.1743
26.68533.10312.62244.62392.29634.22860.1675-0.4228-0.05540.1212-0.1258-0.01140.23790.2073-0.06320.2802-0.0385-0.00460.35680.06460.1864-12.5739-16.973-8.8513
38.9744.4291-6.39024.7416-2.01076.09250.3015-0.54930.27480.8561-0.12220.2926-1.2011-0.3256-0.24030.35020.0628-0.00850.3997-0.04790.2963-26.85477.3232-18.6375
41.3460.432-1.08240.38070.48663.78370.14310.07530.1378-0.0564-0.04890.0044-0.3957-0.0976-0.05640.25560.0273-0.00890.20920.00920.2469-16.419113.1832-46.2987
54.93693.04412.69266.15643.84516.73170.06270.539-0.1586-0.3780.1857-0.2566-0.2730.2785-0.20160.24070.04530.05240.33580.02390.2194-10.92544.0685-64.6535
61.32670.122-0.32221.5451-0.51192.76660.08050.1297-0.0688-0.1617-0.0821-0.01660.1242-0.16070.00120.1610.0315-0.0070.2313-0.01720.1794-17.69110.6089-52.5674
72.0608-1.06022.58511.1657-1.2873.25620.06930.0490.0182-0.0743-0.03050.3858-0.1893-0.7691-0.04730.1950.0953-0.0190.4336-0.0080.2881-32.02755.095-48.5722
84.1459-0.826-1.00934.20131.31363.2055-0.13420.41420.1866-0.7617-0.16590.2242-0.598-0.82010.28350.51170.1888-0.11190.53610.04910.3352-30.480214.3174-63.187
95.2436-1.1059-1.32413.440.6172.56210.12150.49640.21-0.5164-0.0366-0.0155-0.4122-0.0993-0.10750.42360.0585-0.02490.34560.05490.207-15.717913.9312-65.7314
104.8699-3.84055.15025.1055-4.4775.5320.41430.774-0.4138-0.8721-0.01180.61211.1754-0.1788-0.45220.4655-0.0902-0.06980.5248-0.0420.3361-24.625-12.4184-55.3999
117.05170.29284.27130.26560.03044.1652-0.1234-0.25760.06140.12510.0575-0.21630.03430.27870.08570.19390.0096-0.01730.2494-0.01570.2014-11.1422-11.3043-35.3085
124.44751.47431.07085.56770.70066.5150.0443-0.0688-0.4880.0677-0.044-0.10740.8933-0.05670.01890.1966-0.01220.02850.22920.00320.2825-16.0569-21.7703-20.2972
134.722-3.2405-3.12973.90942.6174.7188-0.0842-0.58190.35620.18040.2541-0.1880.03540.3641-0.14020.1547-0.0091-0.03120.3885-0.02650.2117-9.8097-5.9276-9.8367
140.9313-0.25640.41141.0402-0.13941.65550.0353-0.03560.0520.0296-0.01590.0188-0.017-0.0551-0.01090.1586-0.02540.00580.2168-0.00410.2095-16.9783-4.085-22.2305
151.22260.6031-0.83871.8186-1.55632.5340.1193-0.18820.0674-0.02310.13010.41410.2055-0.4394-0.23310.1863-0.0988-0.02830.31660.01190.2655-30.8818-11.2583-25.9342
164.7718-3.51340.47323.0353-2.13487.5911-0.1156-0.43390.47831.3236-0.0415-0.1826-0.3591-0.74180.14120.4101-0.02390.03510.54840.02260.3712-30.486-11.1129-6.93
178.60260.8604-1.25263.60951.59578.6547-0.1899-0.2009-0.77860.339-0.11830.20850.6241-0.20740.28730.276-0.09640.00360.27460.06020.3115-30.3217-22.3393-17.9053
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 219 through 233 )
2X-RAY DIFFRACTION2chain 'B' and (resid 234 through 258 )
3X-RAY DIFFRACTION3chain 'A' and (resid 0 through 20 )
4X-RAY DIFFRACTION4chain 'A' and (resid 21 through 57 )
5X-RAY DIFFRACTION5chain 'A' and (resid 58 through 82 )
6X-RAY DIFFRACTION6chain 'A' and (resid 83 through 146 )
7X-RAY DIFFRACTION7chain 'A' and (resid 147 through 188 )
8X-RAY DIFFRACTION8chain 'A' and (resid 189 through 233 )
9X-RAY DIFFRACTION9chain 'A' and (resid 234 through 258 )
10X-RAY DIFFRACTION10chain 'B' and (resid 0 through 20 )
11X-RAY DIFFRACTION11chain 'B' and (resid 21 through 39 )
12X-RAY DIFFRACTION12chain 'B' and (resid 40 through 57 )
13X-RAY DIFFRACTION13chain 'B' and (resid 58 through 82 )
14X-RAY DIFFRACTION14chain 'B' and (resid 83 through 146 )
15X-RAY DIFFRACTION15chain 'B' and (resid 147 through 188 )
16X-RAY DIFFRACTION16chain 'B' and (resid 189 through 200 )
17X-RAY DIFFRACTION17chain 'B' and (resid 201 through 218 )

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