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Basic information

Entry
Database: PDB / ID: 4lom
TitleCrystal Structure of Mycobacterium tuberculosis HisB in complex with its substrate
ComponentsImidazoleglycerol-phosphate dehydratase
KeywordsLYASE / ENZYME-SUBSTRATE COMPLEX / Dehydratase
Function / homologyImidazole glycerol phosphate dehydratase; domain 1 / Ribosomal Protein S5; domain 2 / 2-Layer Sandwich / Alpha Beta / Chem-IYP / : / :
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAhangar, M.S. / Vyas, R. / Nasir, N. / Biswal, B.K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Crystal structures of the native, substrate- bound and inhibited forms of Mycobacterium tuberculosis imidazole glycerol phosphate dehydratase
Authors: Ahangar, M.S. / Vyas, R. / Nasir, N. / Biswal, B.K.
History
DepositionJul 13, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.process_site
Revision 1.2Nov 8, 2023Group: 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
A: Imidazoleglycerol-phosphate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0365
Polymers23,6341
Non-polymers4034
Water1,31573
1
A: Imidazoleglycerol-phosphate dehydratase
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)576,875120
Polymers567,20424
Non-polymers9,67196
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area82980 Å2
ΔGint-125 kcal/mol
Surface area136050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.514, 112.514, 112.514
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-304-

MN

21A-469-

HOH

31A-473-

HOH

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Components

#1: Protein Imidazoleglycerol-phosphate dehydratase / IGPD


Mass: 23633.516 Da / Num. of mol.: 1 / Fragment: UNP residues 2-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: hisB, RVBD_1601 / Plasmid: pYUB1062 / Production host: Mycobacterium smegmatis (bacteria) / Strain (production host): mc2(4517)
References: UniProt: I6XBW5, imidazoleglycerol-phosphate dehydratase
#2: Chemical ChemComp-IYP / (2R,3S)-2,3-dihydroxy-3-(1H-imidazol-5-yl)propyl dihydrogen phosphate


Mass: 238.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11N2O6P
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG1500, 0.2M Sodium Citrate, 0.1M Tris HCl, 4mM Imidazole Glycerol Phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.1→37.51 Å / Num. obs: 14776 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GQU

4gqu


Resolution: 2.1→37.5 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.359 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24909 746 5 %RANDOM
Rwork0.19604 ---
obs0.19863 14028 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.815 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 18 73 1567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191526
X-RAY DIFFRACTIONr_bond_other_d0.0020.021443
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.9482078
X-RAY DIFFRACTIONr_angle_other_deg0.72733296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.665192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64322.02774
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.57315235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7211518
X-RAY DIFFRACTIONr_chiral_restr0.0620.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211740
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02368
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 59 -
Rwork0.332 978 -
obs--96.92 %

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