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- PDB-6vdg: Crystal Structure of the Y182A HisF Mutant from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 6vdg
TitleCrystal Structure of the Y182A HisF Mutant from Thermotoga maritima
ComponentsImidazole glycerol phosphate synthase subunit HisF
KeywordsLYASE / Cyclase / Histidine Pathway / TIM-Barrel
Function / homology
Function and homology information


imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / L-histidine biosynthetic process / lyase activity / cytoplasm
Similarity search - Function
Histidine biosynthesis, HisF / : / Histidine biosynthesis protein / Histidine biosynthesis protein / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Imidazole glycerol phosphate synthase subunit HisF
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsAlmeida, V.M. / Matsuyama, B.Y. / Farah, C.S. / Marana, S.R.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2016/22365-9 Brazil
Sao Paulo Research Foundation (FAPESP)2018/25952-8 Brazil
Coordination for the Improvement of Higher Education Personnel88882.332977/2019-01 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Role of a high centrality residue in protein dynamics and thermal stability.
Authors: Medeiros Almeida, V. / Chaudhuri, A. / Cangussu Cardoso, M.V. / Matsuyama, B.Y. / Monteiro Ferreira, G. / Goulart Trossini, G.H. / Salinas, R.K. / Loria, J.P. / Marana, S.R.
History
DepositionDec 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 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

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Assembly

Deposited unit
A: Imidazole glycerol phosphate synthase subunit HisF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7432
Polymers27,6481
Non-polymers951
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.624, 95.624, 154.913
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Imidazole glycerol phosphate synthase subunit HisF / IGP synthase cyclase subunit / IGP synthase subunit HisF / ImGP synthase subunit HisF / IGPS subunit HisF


Mass: 27647.750 Da / Num. of mol.: 1 / Mutation: Y182A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: hisF, TM_1036 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X0C6, imidazole glycerol-phosphate synthase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.7 Å3/Da / Density % sol: 66.73 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 23% PEG 3350, 20mM Potassium Phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45851 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45851 Å / Relative weight: 1
ReflectionResolution: 2.79→47.81 Å / Num. obs: 10873 / % possible obs: 98.6 % / Redundancy: 13.3 % / Biso Wilson estimate: 69.97 Å2 / CC1/2: 0.99 / Net I/σ(I): 17.72
Reflection shellResolution: 2.79→2.8 Å / Mean I/σ(I) obs: 1.69 / Num. unique obs: 1635 / CC1/2: 0.835 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1gpw

1gpw


Resolution: 2.79→45.69 Å / SU ML: 0.3883 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1671
RfactorNum. reflection% reflection
Rfree0.2632 1086 10 %
Rwork0.2041 --
obs0.21 10863 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.79→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 5 29 1851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00461864
X-RAY DIFFRACTIONf_angle_d0.732518
X-RAY DIFFRACTIONf_chiral_restr0.0514297
X-RAY DIFFRACTIONf_plane_restr0.0034323
X-RAY DIFFRACTIONf_dihedral_angle_d26.6607689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.920.35631240.26621116X-RAY DIFFRACTION93.16
2.92-3.070.35151340.25531208X-RAY DIFFRACTION99.78
3.07-3.260.32011330.22291203X-RAY DIFFRACTION100
3.26-3.510.29021360.22911219X-RAY DIFFRACTION100
3.51-3.870.30771360.20571219X-RAY DIFFRACTION99.78
3.87-4.430.23041360.17541233X-RAY DIFFRACTION99.13
4.43-5.570.23131400.17681246X-RAY DIFFRACTION99.21

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