PDB-3t78: Crystal Structure of Mycobacterium tuberculosis Indole Glycerol P...

ID or keywords:

Entry

Database: PDB / ID: 3t78

Title

Crystal Structure of Mycobacterium tuberculosis Indole Glycerol Phosphate Synthase (IGPS) in Complex with 5-Fluoroanthranilate

Components

Indole-3-glycerol phosphate synthase

Keywords

LYASE / Indole-3-glycerol Phosphate Synthase (IGPS) / Tryptophan biosynthesis / Structural Genomics / TB Structural Genomics Consortium / TBSGC

Function / homology

Function and homology information

5-phosphoribose 1-diphosphate metabolic process / indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / L-tryptophan biosynthetic process / peptidoglycan-based cell wall / magnesium ion binding / plasma membrane
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.6 Å

Authors

Reddy, M.C.M. / Bruning, J.B. / Thurman, C. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)

Citation

Journal: To be Published
Title: Structural Insights and Inhibition of Mycobacterium tuberculosis Indole Glycerol Phosphate Synthase (IGPS): an Essential Enzyme for Tryptophan Biosynthesis
Authors: Reddy, M.C.M. / Bruning, J.B. / Thurman, C. / Sacchettini, J.C.

History

Deposition	Jul 29, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 8, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.2	Sep 13, 2023	Group: 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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3t78.cif.gz	71.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3t78_validation.pdf.gz	473.4 KB	Display	wwPDB validaton report
Full document	3t78_full_validation.pdf.gz	477.9 KB	Display
Data in XML	3t78_validation.xml.gz	16.1 KB	Display
Data in CIF	3t78_validation.cif.gz	24.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t7/3t78 ftp://data.pdbj.org/pub/pdb/validation_reports/t7/3t78	HTTPS FTP

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Related structure data

Related structure data	3t40C 3t44C 3t55C 1igsS 3qja C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5t5o-4 5t5o-6 5t5p-1 4gaw-7 5t5o-5 4ktu-d 6y4s-1 1tpo-d 2g4u-d 5t5p-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Indole-3-glycerol phosphate synthase

hetero molecules

28.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	46.243, 53.328, 87.406
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Indole-3-glycerol phosphate synthase / IGPS Mass: 28053.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT1646, MTCY01B2.03, Rv1611, trpC / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0A632, UniProt: P9WFX7*PLUS, indole-3-glycerol-phosphate synthase
#2: Chemical	ChemComp-5RG / 2-amino-5-fluorobenzoic acid Mass: 155.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₆FNO₂
#3: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₂O₄
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.92 Å³/Da / Density % sol: 35.97 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1M Sodium acetate trihydrate, 2.0 ammonium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9771 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2009 / Details: mirrors

Radiation

Monochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9771 Å / Relative weight: 1

Reflection

Resolution: 1.6→50 Å / Num. all: 29234 / Num. obs: 29234 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / B_iso Wilson estimate: 12.65 Å² / R_merge(I) obs: 0.066 / R_sym value: 0.066 / Χ²: 1.328 / Net I/σ(I): 11.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	R_sym value	Χ²	% possible all
1.6-1.63	12.9	0.337	8.9	1411	0.337	0.943	99.7
1.63-1.66	13.3	0.326	10.2	1427	0.326	0.997	99.8
1.66-1.69	13.6	0.305	11	1425	0.305	1.016	99.8
1.69-1.72	13.6	0.283	12.3	1467	0.283	1.033	99.9
1.72-1.76	13.9	0.249	14.3	1423	0.249	1.103	99.9
1.76-1.8	14	0.223	17.4	1424	0.223	1.133	99.9
1.8-1.85	14.1	0.203	19.2	1466	0.203	1.172	99.9
1.85-1.9	14.3	0.172	24.5	1443	0.172	1.349	99.9
1.9-1.95	14.5	0.151	27.4	1417	0.151	1.35	99.9
1.95-2.02	14.4	0.127	33.1	1468	0.127	1.501	100
2.02-2.09	14.5	0.108	39.3	1460	0.108	1.36	100
2.09-2.17	14.4	0.092	44.8	1427	0.092	1.29	100
2.17-2.27	14.5	0.087	47.2	1480	0.087	1.471	99.9
2.27-2.39	14.4	0.083	51.8	1449	0.083	1.741	100
2.39-2.54	14.5	0.074	61.3	1477	0.074	1.896	100
2.54-2.74	14.5	0.062	64.2	1476	0.062	1.594	100
2.74-3.01	14.3	0.049	71.96	1472	0.049	1.454	99.9
3.01-3.45	14.1	0.04	80.6	1489	0.04	1.425	100
3.45-4.34	13.8	0.033	86.9	1519	0.033	1.337	99.9
4.34-50	13.4	0.031	88.8	1614	0.031	1.224	99.6

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
PHENIX		refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1IGS

1igs

Resolution: 1.6→45.5239 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8968 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: mlhl

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1907	1453	5.08 %	random
R_work	0.1596	-	-	-
all	-	28611	-	-
obs	-	28611	97.78 %	-

Solvent computation

B_sol: 67.205 Å² / k_sol: 0.382 e/Å³

Displacement parameters

B_iso max: 106.18 Å² / B_iso mean: 18.1266 Å² / B_iso min: 3.95 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.509 Å²	-0 Å²	-0 Å²
2-	-	-0.769 Å²	-0 Å²
3-	-	-	-3.741 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→45.5239 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1846	0	30	345	2221

Refine LS restraints

Refine-ID	Type	Dev ideal	Weight
X-RAY DIFFRACTION	f_angle_d	0.781	1
X-RAY DIFFRACTION	f_bond_d	0.005	1
X-RAY DIFFRACTION	f_chiral_restr	0.054	1
X-RAY DIFFRACTION	f_dihedral_angle_d	8.644	1
X-RAY DIFFRACTION	f_plane_restr	0.004	1
X-RAY DIFFRACTION	f_nbd_refined	4.059	1

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Total num. of bins used	% reflection obs (%)
1.6-1.6094	0.1667	413	X-RAY DIFFRACTION	54	80
1.6094-1.6196	0.1568	477	X-RAY DIFFRACTION	54	91
1.6196-1.6301	0.154	485	X-RAY DIFFRACTION	54	90
1.6301-1.6409	0.1513	478	X-RAY DIFFRACTION	54	88
1.6409-1.652	0.15	510	X-RAY DIFFRACTION	54	90
1.652-1.6634	0.1667	443	X-RAY DIFFRACTION	54	89
1.6634-1.6751	0.1587	496	X-RAY DIFFRACTION	54	91
1.6751-1.6872	0.1616	453	X-RAY DIFFRACTION	54	89
1.6872-1.6996	0.1534	493	X-RAY DIFFRACTION	54	93
1.6996-1.7124	0.1589	495	X-RAY DIFFRACTION	54	90
1.7124-1.7255	0.1622	486	X-RAY DIFFRACTION	54	90
1.7255-1.7391	0.1457	466	X-RAY DIFFRACTION	54	92
1.7391-1.7531	0.1616	496	X-RAY DIFFRACTION	54	92
1.7531-1.7676	0.1709	515	X-RAY DIFFRACTION	54	92
1.7676-1.7826	0.1459	488	X-RAY DIFFRACTION	54	92
1.7826-1.7981	0.1568	483	X-RAY DIFFRACTION	54	93
1.7981-1.8142	0.1627	514	X-RAY DIFFRACTION	54	94
1.8142-1.8308	0.1683	495	X-RAY DIFFRACTION	54	94
1.8308-1.8481	0.1579	494	X-RAY DIFFRACTION	54	92
1.8481-1.866	0.1605	502	X-RAY DIFFRACTION	54	93
1.866-1.8847	0.141	478	X-RAY DIFFRACTION	54	93
1.8847-1.9041	0.1545	521	X-RAY DIFFRACTION	54	92
1.9041-1.9244	0.1512	474	X-RAY DIFFRACTION	54	92
1.9244-1.9455	0.1521	497	X-RAY DIFFRACTION	54	92
1.9455-1.9676	0.157	500	X-RAY DIFFRACTION	54	94
1.9676-1.9908	0.1542	498	X-RAY DIFFRACTION	54	94
1.9908-2.015	0.1562	507	X-RAY DIFFRACTION	54	94
2.015-2.0406	0.1435	485	X-RAY DIFFRACTION	54	92
2.0406-2.0674	0.1608	500	X-RAY DIFFRACTION	54	93
2.0674-2.0957	0.1451	524	X-RAY DIFFRACTION	54	94
2.0957-2.1257	0.1511	507	X-RAY DIFFRACTION	54	93
2.1257-2.1574	0.1541	503	X-RAY DIFFRACTION	54	94
2.1574-2.1911	0.1466	500	X-RAY DIFFRACTION	54	95
2.1911-2.227	0.1591	527	X-RAY DIFFRACTION	54	95
2.227-2.2654	0.1596	485	X-RAY DIFFRACTION	54	95
2.2654-2.3066	0.1606	517	X-RAY DIFFRACTION	54	93
2.3066-2.351	0.1536	498	X-RAY DIFFRACTION	54	92
2.351-2.399	0.1468	497	X-RAY DIFFRACTION	54	94
2.399-2.4511	0.1597	514	X-RAY DIFFRACTION	54	93
2.4511-2.5081	0.1641	507	X-RAY DIFFRACTION	54	94
2.5081-2.5709	0.1635	523	X-RAY DIFFRACTION	54	96
2.5709-2.6404	0.1704	509	X-RAY DIFFRACTION	54	95
2.6404-2.718	0.1595	528	X-RAY DIFFRACTION	54	95
2.718-2.8058	0.1754	516	X-RAY DIFFRACTION	54	94
2.8058-2.906	0.1743	511	X-RAY DIFFRACTION	54	95
2.906-3.0224	0.1579	519	X-RAY DIFFRACTION	54	94
3.0224-3.1599	0.1471	524	X-RAY DIFFRACTION	54	95
3.1599-3.3264	0.1424	528	X-RAY DIFFRACTION	54	95
3.3264-3.5348	0.1416	536	X-RAY DIFFRACTION	54	94
3.5348-3.8076	0.1446	519	X-RAY DIFFRACTION	54	95
3.8076-4.1905	0.1354	541	X-RAY DIFFRACTION	54	96
4.1905-4.7963	0.1395	533	X-RAY DIFFRACTION	54	95
4.7963-6.0406	0.1811	557	X-RAY DIFFRACTION	54	95
6.0406-45.5423	0.1978	593	X-RAY DIFFRACTION	54	96

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