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- PDB-5yht: Crystal structure of a phosphatase from Mycobacterium tuberculosi... -

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Basic information

Entry
Database: PDB / ID: 5yht
TitleCrystal structure of a phosphatase from Mycobacterium tuberculosis in complex with its substrate
ComponentsHistidinol-phosphatase
KeywordsHYDROLASE / Mycobacterium tuberculosis / phosphatase / histidinol / enzyme activity
Function / homology
Function and homology information


Mycothiol biosynthesis / phosphoric ester hydrolase activity / mycothiol biosynthetic process / histidinol-phosphatase / histidinol-phosphatase activity / inositol monophosphate 1-phosphatase activity / L-histidine biosynthetic process / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Histidinol-phosphate phosphatase, putative, inositol monophosphatase / Inositol monophosphatase, metal-binding site / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HSA / L-histidinol / PHOSPHATE ION / Histidinol-phosphatase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsBiswal, B.K. / Jha, B.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology India
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Identification and structural characterization of a histidinol phosphate phosphatase fromMycobacterium tuberculosis
Authors: Jha, B. / Kumar, D. / Sharma, A. / Dwivedy, A. / Singh, R. / Biswal, B.K.
History
DepositionSep 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 11, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Nov 22, 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_ncs_dom_lim
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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidinol-phosphatase
B: Histidinol-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,21411
Polymers57,3042
Non-polymers9109
Water41423
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The functional unit of the enzyme is a dimer. There are 4 such dimers in an asymmetric unit. Therefore, no symmetry operation is required to generate a functional unit.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.664, 142.446, 48.723
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 1 / Auth seq-ID: 5 - 258 / Label seq-ID: 12 - 265

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.084333, 0.755885, 0.649251), (0.757441, -0.374729, 0.53466), (0.647434, 0.536858, -0.540936)33.64782, 66.459709, -125.131538
3given(1), (1), (1)
4given(-0.999994, 0.000673, 0.003325), (0.000674, 1, 0.000243), (-0.003325, 0.000245, -0.999994)33.56509, 46.295471, -100.946716
5given(1), (1), (1)
6given(0.084727, 0.75507, -0.650146), (-0.756568, -0.375854, -0.535106), (-0.648403, 0.537218, 0.539417)0.2091, 20.38658, -24.046659
7given(1), (1), (1)
8given(0.084788, -0.755804, 0.649285), (-0.756078, 0.375612, 0.535968), (-0.648967, -0.536353, -0.539599)20.42193, 35.942169, -39.491451
9given(1), (1), (1)
10given(-1, -0.000472, 0.000765), (0.000472, -1, 5.0E-6), (0.000765, 6.0E-6, 1)33.476582, 47.376331, -71.186447
11given(1), (1), (1)
12given(-0.083435, -0.75647, -0.648684), (0.756795, 0.375392, -0.535109), (0.648305, -0.535568, 0.541172)15.08734, 50.132038, -108.475113
13given(1), (1), (1)
14given(1, -5.0E-6, 0.000623), (-4.0E-6, -1, -0.00074), (0.000623, 0.00074, -1)-0.09949, 1.12237, -29.775221
15given(1), (1), (1)
16given(0.082742, 0.757589, -0.647467), (-0.75779, -0.37412, -0.534592), (-0.647231, 0.534877, 0.543138)0.3939, 20.471069, -23.920549
17given(1), (1), (1)
18given(-1, 0.000651, -0.000258), (0.000651, 0.999997, -0.00243), (0.000256, -0.00243, -0.999997)33.42329, 46.183369, -101.014328
19given(1), (1), (1)
20given(-1, 0.000108, 0.000986), (-0.000107, -1, 0.000671), (0.000986, 0.000671, 0.999999)33.47596, 47.382252, -71.216988
21given(1), (1), (1)
22given(0.08517, -0.757331, 0.647453), (-0.755623, 0.374464, 0.537412), (-0.649446, -0.535002, -0.540364)20.484209, 35.981411, -39.493919
23given(1), (1), (1)
24given(0.999999, 0.001106, 0.000155), (0.001105, -0.999999, 0.000587), (0.000156, -0.000587, -1)-0.03483, 1.03682, -29.78964
25given(1), (1), (1)
26given(-0.084034, -0.756878, -0.648131), (0.756084, 0.375235, -0.536224), (0.649058, -0.535102, 0.540731)15.10329, 50.18145, -108.422981
27given(1), (1), (1)
28given(-0.083094, -0.757008, 0.648101), (-0.756738, -0.375229, -0.535305), (0.648416, -0.534923, -0.541677)33.089531, -25.906139, -77.015312
29given(1), (1), (1)
30given(-0.083055, 0.7579, -0.647062), (-0.756269, 0.374904, 0.536195), (0.648968, 0.533887, 0.542038)12.92933, -10.34344, -61.50209
31given(1), (1), (1)
32given(0.999992, -0.000257, -0.004065), (-0.000255, -1, 0.000349), (-0.004065, -0.000348, -0.999992)-0.00967, 1.08843, -29.75897
33given(1), (1), (1)
34given(0.081895, 0.758554, 0.646444), (0.756827, 0.374694, -0.535554), (-0.648465, 0.533105, -0.543408)18.50687, 3.82241, 7.46682
35given(1), (1), (1)
36given(-0.999996, -0.000617, 0.002846), (0.000614, -0.999999, -0.001007), (0.002847, -0.001006, 0.999995)33.394211, -45.176289, -71.299057
37given(1), (1), (1)
38given(1, -0.000319, -0.000106), (-0.000319, -1, -0.000635), (-0.000106, 0.000635, -1)-0.0655, 1.09403, -29.801069
39given(1), (1), (1)
40given(-0.085524, 0.75649, -0.64839), (-0.754865, 0.375544, 0.537722), (0.65028, 0.535435, 0.53893)12.96478, -10.35014, -61.500149
41given(1), (1), (1)
42given(-0.999999, -0.000955, -0.000966), (0.000953, -0.999997, 0.00223), (-0.000968, 0.002229, 0.999997)33.490959, -45.31036, -71.126694
43given(1), (1), (1)
44given(0.084328, 0.756135, 0.64896), (0.755294, 0.3763, -0.536591), (-0.649939, 0.535405, -0.539371)18.26738, 3.94166, 7.41495
45given(1), (1), (1)
46given(-0.085618, 0.756013, -0.648933), (0.755564, -0.375297, -0.536912), (-0.649456, -0.53628, -0.539084)13.03219, 11.42807, 31.709881
47given(1), (1), (1)
48given(-0.999999, -0.000569, -0.00126), (-0.000568, 0.999999, -0.001138), (0.001261, -0.001137, -0.999999)33.576302, 46.364719, 41.368351
49given(1), (1), (1)
50given(0.084432, 0.755629, 0.649535), (-0.756124, -0.375962, 0.535658), (0.648959, -0.536356, 0.539606)18.282181, -2.78322, -37.228481
51given(1), (1), (1)
52given(0.08426, 0.756121, 0.648985), (-0.75675, -0.375156, 0.535339), (0.648251, -0.536227, 0.540584)18.355709, -2.74946, -37.300991
53given(1), (1), (1)
54given(-0.999999, -0.000409, -0.001338), (-0.00041, 1, 0.000689), (0.001338, 0.00069, -0.999999)33.586121, 46.270229, 41.387199
55given(1), (1), (1)
56given(-0.083251, -0.756229, -0.648989), (-0.756853, -0.375669, 0.534833), (-0.648262, 0.535715, -0.541079)15.21094, -49.053619, 78.667969

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Histidinol-phosphatase / HolPase / Histidinol-phosphate phosphatase


Mass: 28652.160 Da / Num. of mol.: 2 / Fragment: UNP residues 2-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: hisN, impC, Rv3137 / Production host: Mycobacterium smegmatis (bacteria) / References: UniProt: P95189, histidinol-phosphatase

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Non-polymers , 5 types, 32 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HSA / PHOSPHORIC ACID MONO-[2-AMINO-3-(3H-IMIDAZOL-4-YL)-PROPYL]ESTER


Mass: 221.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12N3O4P
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-HSO / L-histidinol


Type: L-peptide linking / Mass: 142.179 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12N3O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.87 Å3/Da / Density % sol: 57.19 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 1 M Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.9→142.37 Å / Num. obs: 14904 / % possible obs: 99.2 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 12.74
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2 / Num. unique obs: 1464 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZON

5zon


Resolution: 2.87→77.8 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.904 / SU B: 18.739 / SU ML: 0.344 / Cross valid method: THROUGHOUT / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27876 1098 7.4 %RANDOM
Rwork0.22929 ---
obs0.23303 13776 96.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.414 Å2
Baniso -1Baniso -2Baniso -3
1-1.86 Å20 Å2-0 Å2
2---1.2 Å20 Å2
3----0.66 Å2
Refinement stepCycle: 1 / Resolution: 2.87→77.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3425 0 43 23 3491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193539
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9494818
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2145496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77522.143112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.82215429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.941531
X-RAY DIFFRACTIONr_chiral_restr0.1020.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212709
X-RAY DIFFRACTIONr_gen_planes_other
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_it4.7656.5172007
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.4879.7582495
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.9656.3191532
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined13.43914738
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 1596 / Type: tight thermal / Rms dev position: 9.51 Å / Weight position: 0.5
LS refinement shellResolution: 2.869→2.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 41 -
Rwork0.318 626 -
obs--60.42 %

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