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- PDB-2a0n: Crystal structure of Imidazole glycerol phosphate synthase subuni... -

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Basic information

Entry
Database: PDB / ID: 2a0n
TitleCrystal structure of Imidazole glycerol phosphate synthase subunit hisF (EC 4.1.3.-) (tm1036) from Thermotoga maritima at 1.64 A resolution
ComponentsImidazole glycerol phosphate synthase subunit hisF
KeywordsLYASE / tm1036 / Imidazole glycerol phosphate synthase subunit hisF / EC 4.1.3.- / IGP / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
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
IODIDE ION / PHOSPHATE ION / Unknown ligand / Imidazole glycerol phosphate synthase subunit HisF
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Imidazole glycerol phosphate synthase subunit hisF (EC 4.1.3.-) (tm1036) from Thermotoga maritima at 1.64 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,19910
Polymers29,2161
Non-polymers9839
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.610, 96.610, 155.828
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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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: 29215.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: hisF / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X0C6, Lyases; Carbon-carbon lyases; Oxo-acid-lyases
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.29 Å3/Da / Density % sol: 62.33 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.9
Details: 0.2None Nal, 20.0% PEG-3350, No Buffer, pH 6.9, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979748
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2004
Details: Flat Mirror; Side-deflecting monochromator (Si 111)
RadiationMonochromator: Flat Mirror; Side-deflecting monochromator (Si 111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979748 Å / Relative weight: 1
ReflectionResolution: 1.64→48.31 Å / Num. obs: 53271 / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 6.2
Reflection shell

Rmerge(I) obs: 0.014 / Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Mean I/σ(I) obsNum. measured obsRsym value
1.64-1.6810010.60.538370.01369
1.68-1.7310010.60.737750.01057
1.73-1.7810010.60.936590.852
1.78-1.8310010.61.235760.637
1.83-1.8910010.61.534850.514
1.89-1.9610010.61.933110.397
1.96-2.0310010.62.532570.301
2.03-2.1210010.53.331260.228
2.12-2.2110010.54.230080.179
2.21-2.3210010.55.228830.143
2.32-2.4410010.95.627440.13
2.44-2.5910013.75.226050.136
2.59-2.7710015.5624700.117
2.77-2.9910018.56.623050.103
2.99-3.2810020.57.621310.08
3.28-3.6710020.29.819400.064
3.67-4.2310019.111.517360.053
4.23-5.1910020.412.814920.045
5.19-7.3310019.511.711990.052
7.33-48.3199.716.912.57320.046

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0001refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1vh7

1vh7


Resolution: 1.64→48.31 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.353 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE ADDITIONAL DENSITY NEAR CYS-9 HAS BEEN MODELED AS AN UNL, UNKNOWN LIGAND. THIS RESIDUE IS COVALENTLY BOUND TO SG OF CYS-9.
RfactorNum. reflection% reflectionSelection details
Rfree0.192 2704 5.1 %RANDOM
Rwork0.167 ---
all0.168 ---
obs-50488 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.454 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.64→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 42 279 2236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222018
X-RAY DIFFRACTIONr_bond_other_d0.0030.021918
X-RAY DIFFRACTIONr_angle_refined_deg1.9081.9762724
X-RAY DIFFRACTIONr_angle_other_deg1.69934433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2135256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28124.52484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.1515362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1611512
X-RAY DIFFRACTIONr_chiral_restr0.0990.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022257
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02417
X-RAY DIFFRACTIONr_nbd_refined0.2410.2421
X-RAY DIFFRACTIONr_nbd_other0.1940.22068
X-RAY DIFFRACTIONr_nbtor_other0.0960.21188
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2190
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0860.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1810.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.224
X-RAY DIFFRACTIONr_mcbond_it1.90131266
X-RAY DIFFRACTIONr_mcbond_other0.5553527
X-RAY DIFFRACTIONr_mcangle_it3.0452031
X-RAY DIFFRACTIONr_scbond_it5.0078798
X-RAY DIFFRACTIONr_scangle_it7.14811693
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.31 204
Rwork0.266 3630
Refinement TLS params.Method: refined / Origin x: 22.2282 Å / Origin y: 79.1115 Å / Origin z: 37.306 Å
111213212223313233
T-0.0745 Å2-0.0031 Å20.0254 Å2--0.0361 Å20.0032 Å2---0.0531 Å2
L1.5126 °2-0.1393 °2-0.0954 °2-0.6465 °20.0937 °2--0.8217 °2
S0.0412 Å °-0.1588 Å °0.1606 Å °0.0671 Å °-0.0102 Å °0.0454 Å °-0.0769 Å °-0.0755 Å °-0.0311 Å °
Refinement TLS groupSelection: all

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