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- PDB-4ewn: Structure of HisF-D130V+D176V with bound rCdRP -

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Basic information

Entry
Database: PDB / ID: 4ewn
TitleStructure of HisF-D130V+D176V with bound rCdRP
ComponentsImidazole glycerol phosphate synthase subunit HisF
KeywordsLYASE
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
Chem-0VR / Imidazole glycerol phosphate synthase subunit HisF
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å
AuthorsReisinger, B. / Bocola, M. / Rajendran, C. / List, F. / Sterner, R.
CitationJournal: Protein Eng.Des.Sel. / Year: 2012
Title: A sugar isomerization reaction established on various (beta-alpha)8-barrel scaffolds is based on substrate-assisted catalysis
Authors: Reisinger, B. / Bocola, M. / List, F. / Claren, J. / Rajendran, C. / Sterner, R.
History
DepositionApr 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,0732
Polymers27,7221
Non-polymers3511
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.654, 112.517, 163.402
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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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: 27721.957 Da / Num. of mol.: 1 / Mutation: D130V-D176V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: hisF, TM_1036 / Plasmid: pET / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X0C6, Lyases; Carbon-carbon lyases; Oxo-acid-lyases
#2: Chemical ChemComp-0VR / 1-(O-carboxy-phenylamino)-1-deoxy-D-ribulose-5-phosphate / 1-[(2-carboxyphenyl)amino]-1-deoxy-5-O-phosphono-D-ribitol


Mass: 351.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18NO9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.56 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationMonochromator: Diamond(001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→81.701 Å / Num. all: 21106 / Num. obs: 20607 / % possible obs: 95.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.2_869) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.903→46.336 Å / SU ML: 0.77 / σ(F): 1.99 / Phase error: 34.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 1027 4.99 %RANDOM
Rwork0.2038 ---
obs0.2055 20574 97.49 %-
all-20802 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.42 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.608 Å20 Å2-0 Å2
2---0.1322 Å20 Å2
3----1.4758 Å2
Refinement stepCycle: LAST / Resolution: 1.903→46.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 23 66 1961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071920
X-RAY DIFFRACTIONf_angle_d1.0792590
X-RAY DIFFRACTIONf_dihedral_angle_d14.642708
X-RAY DIFFRACTIONf_chiral_restr0.071306
X-RAY DIFFRACTIONf_plane_restr0.003328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.903-2.00280.54061300.53042473X-RAY DIFFRACTION88
2.0028-2.12830.36551470.36682795X-RAY DIFFRACTION98
2.1283-2.29260.3441420.26542745X-RAY DIFFRACTION96
2.2926-2.52330.2881500.2272833X-RAY DIFFRACTION100
2.5233-2.88840.28021510.21872869X-RAY DIFFRACTION100
2.8884-3.63890.23991500.18682864X-RAY DIFFRACTION100
3.6389-46.34950.16731570.15772968X-RAY DIFFRACTION100
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)
15.2774-0.5818-0.75496.7291-1.62686.88690.08250.11650.1404-0.4664-0.3219-1.09440.27810.90980.23110.32810.0768-0.01970.391-0.02820.427523.10119.820314.9068
28.7058-1.0971.58486.6742-1.38816.2178-0.00011.1208-0.1775-0.8054-0.0424-0.18160.50010.02650.11850.4537-0.0243-0.0820.4086-0.06780.26512.579110.51565.3826
32.85180.41160.48396.42190.63794.57020.13110.12160.1392-0.04980.13530.591-0.1438-0.4952-0.16740.17340.0163-0.03240.28440.05820.29142.619120.379516.7732
44.7392-1.41841.85144.9364-1.79115.905-0.2108-0.0059-0.00250.50960.1819-0.0577-0.13270.1715-0.07270.2723-0.0638-0.01150.2107-0.00440.19511.427411.562228.5963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resseq 2:60)
2X-RAY DIFFRACTION2chain 'D' and (resseq 61:94)
3X-RAY DIFFRACTION3chain 'D' and (resseq 95:152)
4X-RAY DIFFRACTION4chain 'D' and (resseq 153:250)

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