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- PDB-8wmp: Crystal Structure of Mutant HisB from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 8wmp
TitleCrystal Structure of Mutant HisB from Mycobacterium tuberculosis
ComponentsImidazoleglycerol-phosphate dehydratase
KeywordsLYASE / Mutant
Function / homology
Function and homology information


imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / L-histidine biosynthetic process / cytoplasm
Similarity search - Function
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-type fold
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Imidazoleglycerol-phosphate dehydratase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsTiwari, S. / Mohini, M. / Ahmad, M. / Pal, R.K. / Biswal, B.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: To Be Published
Title: Crystal Structure of Mutant HisB from Mycobacterium tuberculosis
Authors: Tiwari, S. / Mohini, M. / Ahmad, M. / Kumar, D. / Pal, R.K. / Biswal, B.K.
History
DepositionOct 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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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)24,0466
Polymers23,7331
Non-polymers3145
Water3,567198
1
A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)577,108144
Polymers569,58424
Non-polymers7,524120
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
Unit cell
Length a, b, c (Å)112.537, 112.537, 112.537
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-303-

CL

21A-507-

HOH

31A-551-

HOH

41A-567-

HOH

51A-571-

HOH

61A-574-

HOH

71A-588-

HOH

81A-589-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Imidazoleglycerol-phosphate dehydratase


Mass: 23732.648 Da / Num. of mol.: 1 / Mutation: E12Q,C131A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: hisB / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0A0T7LD88

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Non-polymers , 5 types, 203 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 1500, sodium citrate tribasic dehydrate, tris HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.75→35 Å / Num. obs: 25208 / % possible obs: 100 % / Redundancy: 44.1 % / CC1/2: 1 / Net I/σ(I): 45.4
Reflection shellResolution: 1.75→1.81 Å / Num. unique obs: 2467 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KHH

6khh


Resolution: 1.75→26.53 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1693 1236 4.92 %
Rwork0.1492 --
obs0.1502 25135 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→26.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 0 14 198 1679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017
X-RAY DIFFRACTIONf_angle_d1.438
X-RAY DIFFRACTIONf_dihedral_angle_d6.79226
X-RAY DIFFRACTIONf_chiral_restr0.115241
X-RAY DIFFRACTIONf_plane_restr0.016278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.820.42241150.35652584X-RAY DIFFRACTION99
1.82-1.90.21921320.19192586X-RAY DIFFRACTION100
1.9-20.17231460.14212590X-RAY DIFFRACTION100
2-2.130.17741390.14672617X-RAY DIFFRACTION100
2.13-2.290.18551400.15392617X-RAY DIFFRACTION100
2.29-2.520.1621310.14592643X-RAY DIFFRACTION100
2.52-2.890.16281370.14212667X-RAY DIFFRACTION100
2.89-3.640.15781510.13262704X-RAY DIFFRACTION100
3.64-26.530.14541450.13772891X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -21.847 Å / Origin y: 10.4834 Å / Origin z: 37.6134 Å
111213212223313233
T0.1348 Å2-0.0003 Å20.0108 Å2-0.136 Å2-0.0028 Å2--0.1095 Å2
L0.3482 °2-0.0837 °2-0.0125 °2-0.4997 °2-0.3317 °2--0.6736 °2
S-0.004 Å °-0.0031 Å °0.0082 Å °0.0738 Å °0.0425 Å °0.0533 Å °-0.0104 Å °-0.0707 Å °-0 Å °
Refinement TLS groupSelection details: all

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