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- PDB-1rhy: Crystal structure of Imidazole Glycerol Phosphate Dehydratase -

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Basic information

Entry
Database: PDB / ID: 1rhy
TitleCrystal structure of Imidazole Glycerol Phosphate Dehydratase
ComponentsImidazole glycerol phosphate dehydratase
KeywordsLYASE / dehydratases / histidine biosynthesis / left-handed b-a-b crossover motif / gene duplication
Function / homology
Function and homology information


imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / L-histidine biosynthetic process
Similarity search - Function
Imidazole glycerol phosphate dehydratase; domain 1 / Imidazoleglycerol-phosphate dehydratase signature 1. / Imidazoleglycerol-phosphate dehydratase / Imidazoleglycerol-phosphate dehydratase, conserved site / Imidazole glycerol phosphate dehydratase domain superfamily / Imidazoleglycerol-phosphate dehydratase / Imidazoleglycerol-phosphate dehydratase signature 2. / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / ETHYL MERCURY ION / : / Imidazoleglycerol-phosphate dehydratase / Imidazoleglycerol-phosphate dehydratase
Similarity search - Component
Biological speciesFilobasidiella neoformans (Cryptococcus neoformans serotype A)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSinha, S.C. / Chaudhuri, B.N. / Burgner, J.W. / Yakovleva, G. / Davisson, V.J. / Smith, J.L.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of imidazole glycerol-phosphate dehydratase: duplication of an unusual fold
Authors: Sinha, S.C. / Chaudhuri, B.N. / Burgner, J.W. / Yakovleva, G. / Davisson, V.J. / Smith, J.L.
History
DepositionNov 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_conn.ptnr2_label_seq_id / _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: Imidazole glycerol phosphate dehydratase
B: Imidazole glycerol phosphate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,88127
Polymers44,0162
Non-polymers2,86525
Water4,450247
1
A: Imidazole glycerol phosphate dehydratase
hetero molecules

A: Imidazole glycerol phosphate dehydratase
hetero molecules

A: Imidazole glycerol phosphate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,14524
Polymers66,0243
Non-polymers3,12121
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area7700 Å2
ΔGint-231 kcal/mol
Surface area22060 Å2
MethodPISA, PQS
2
B: Imidazole glycerol phosphate dehydratase
hetero molecules

B: Imidazole glycerol phosphate dehydratase
hetero molecules

B: Imidazole glycerol phosphate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,49957
Polymers66,0243
Non-polymers5,47554
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area10280 Å2
ΔGint-195 kcal/mol
Surface area24950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.275, 105.275, 105.275
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Cell settingcubic
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-5588-

HOH

21B-9559-

HOH

31B-9588-

HOH

41B-9608-

HOH

51B-9610-

HOH

61B-9630-

HOH

DetailsThe biological assembly is a trimer which can be generated from either subunit in the asymmetric unit by the crystallographic three-fold axis, described by the operators x,y,z; y,z,x and z,x,y.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Imidazole glycerol phosphate dehydratase / E.C.4.2.1.19 / IGPD


Mass: 22008.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Filobasidiella neoformans (Cryptococcus neoformans serotype A)
Gene: HIS3 / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P40919, UniProt: P0CO22*PLUS, imidazoleglycerol-phosphate dehydratase

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Non-polymers , 6 types, 272 molecules

#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-EMC / ETHYL MERCURY ION


Mass: 229.651 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5Hg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.21 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ammonium sulfate, sodium acetate,, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.0086, 1.0078, 0.9150
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1997
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00861
21.00781
30.9151
ReflectionResolution: 2.3→20 Å / Num. all: 17553 / Num. obs: 17324 / % possible obs: 98.7 % / Observed criterion σ(I): 1 / Redundancy: 10 % / Biso Wilson estimate: 31.3 Å2 / Rsym value: 0.066 / Net I/σ(I): 17.8

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Processing

Software
NameVersionClassification
XDSdata scaling
SCALEPACKdata scaling
SOLVEphasing
DMmodel building
CNS1refinement
XDSdata reduction
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→19.55 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2905924.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 878 5.1 %RANDOM
Rwork0.189 ---
all0.1891 17531 --
obs0.1891 17078 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 75.3375 Å2 / ksol: 0.364137 e/Å3
Displacement parametersBiso mean: 46.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 109 247 3113
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_mcbond_it3.433.5
X-RAY DIFFRACTIONc_mcangle_it5.154
X-RAY DIFFRACTIONc_scbond_it5.995
X-RAY DIFFRACTIONc_scangle_it8.115.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 162 5.8 %
Rwork0.245 2637 -
obs-2964 97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ACYGOL.PARACYGOL.TOP
X-RAY DIFFRACTION4HGLIGS.PARHGLIGS.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP

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