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- PDB-1j5t: Crystal structure of indole-3-glycerol phosphate synthase (TM0140... -

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Basic information

Entry
Database: PDB / ID: 1j5t
TitleCrystal structure of indole-3-glycerol phosphate synthase (TM0140) from Thermotoga maritima at 3.0 A resolution
ComponentsINDOLE-3-GLYCEROL PHOSPHATE SYNTHASE
KeywordsLYASE / TM0140 / STRUCTURAL GENOMICS / JCSG / INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
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
Indole-3-glycerol phosphate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of indole-3-glycerol phosphate synthase (TM0140) from Thermotoga maritima at 3.0 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 18, 2018Group: Advisory / Data collection / Database references
Category: pdbx_database_related / pdbx_unobs_or_zero_occ_atoms
Revision 1.4Jan 25, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)27,5803
Polymers27,5091
Non-polymers712
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE
hetero molecules

A: INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE
hetero molecules

A: INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE
hetero molecules

A: INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,31912
Polymers110,0354
Non-polymers2848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_556y,x,-z+11
Buried area12000 Å2
ΔGint-132 kcal/mol
Surface area36600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)117.5966, 117.5966, 82.1529
Angle α, β, γ (deg.)90, 90, 90
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE / IGPS


Mass: 27508.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0140 / Production host: Escherichia coli (E. coli)
References: UniProt: Q56319, indole-3-glycerol-phosphate synthase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 293 K / pH: 5.2
Details: 50% PEG 200, 0.1M phosphate-Citrate ph 4.2, 0.2M NaCl, pH 5.2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K, pH 5.20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97591
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2001 / Details: FLAT MIRROR
RadiationMonochromator: SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97591 Å / Relative weight: 1
ReflectionResolution: 3→44.293 Å / Num. obs: 6026 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 57.9 Å2 / Rsym value: 0.068 / Net I/σ(I): 21
Reflection shellResolution: 3→3.08 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 6.3 / Rsym value: 0.332 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CCP4data reduction
MOLREPphasing
CCP4model building
CNS1.1refinement
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→44.29 Å / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: STANDARD CNS DICTIONARY/ENGH AND HUBER
Details: THE RESIDUES HHH ARE ADDED TO AMINO TERMINUS OF THE SEQUENCE. DISORDERED AND PARTLY DISORDERED SIDECHAINS: 12,25,35,36,37,38,51,62,63,66,93, 111,119,120,123, ...Details: THE RESIDUES HHH ARE ADDED TO AMINO TERMINUS OF THE SEQUENCE. DISORDERED AND PARTLY DISORDERED SIDECHAINS: 12,25,35,36,37,38,51,62,63,66,93, 111,119,120,123, 126,139,142,146,150,164,165,166,173, 181,191,202,213,226
RfactorNum. reflection% reflectionSelection details
Rfree0.297 339 5.6 %RANDOM
Rwork0.24 ---
obs0.24 6019 99.9 %-
all-6027 --
Solvent computationSolvent model: BULK SOLVENT CORRECTION / Bsol: 36.28 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 58 Å2
Baniso -1Baniso -2Baniso -3
1--1.162 Å20 Å20 Å2
2---3.382 Å20 Å2
3---4.544 Å2
Refine analyzeLuzzati coordinate error obs: 0.58 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 3→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1859 0 2 6 1867
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.48
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.6841.5
X-RAY DIFFRACTIONc_mcangle_it3.0282
X-RAY DIFFRACTIONc_scbond_it1.9992
X-RAY DIFFRACTIONc_scangle_it3.3962.5
LS refinement shellResolution: 3→3.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4452 34 4.7 %
Rwork0.3406 689 -

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