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- PDB-5zon: Histidinol phosphate phosphatase from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 5zon
TitleHistidinol phosphate phosphatase from Mycobacterium tuberculosis
ComponentsHistidinol-phosphatase
KeywordsHYDROLASE / phosphatase / histidine biosynthetic pathway
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
PHOSPHATE ION / Histidinol-phosphatase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsJha, B. / Kumar, D. / Biswal, B.K.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Identification and structural characterization of a histidinol phosphate phosphatase from Mycobacterium tuberculosis
Authors: Jha, B. / Kumar, D. / Sharma, A. / Dwivedy, A. / Singh, R. / Biswal, B.K.
History
DepositionApr 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 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
C: Histidinol-phosphatase
D: Histidinol-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,07622
Polymers114,6094
Non-polymers1,46718
Water17,493971
1
A: Histidinol-phosphatase
B: Histidinol-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,94610
Polymers57,3042
Non-polymers6428
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-192 kcal/mol
Surface area18410 Å2
MethodPISA
2
C: Histidinol-phosphatase
D: Histidinol-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,13012
Polymers57,3042
Non-polymers82610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-195 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.030, 71.062, 91.586
Angle α, β, γ (deg.)92.16, 96.16, 101.94
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPAA4 - 25811 - 265
21ASPASPBB4 - 25811 - 265
12HISHISAA3 - 25810 - 265
22HISHISCC3 - 25810 - 265
13HISHISAA3 - 25810 - 265
23HISHISDD3 - 25810 - 265
14ASPASPBB4 - 25811 - 265
24ASPASPCC4 - 25811 - 265
15ASPASPBB4 - 25811 - 265
25ASPASPDD4 - 25811 - 265
16HISHISCC3 - 25810 - 265
26HISHISDD3 - 25810 - 265

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 28652.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: hisN, impC, Rv3137 / Production host: Mycobacterium smegmatis (bacteria) / References: UniProt: P95189, histidinol-phosphatase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 971 / 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: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 1M ammonium sulfate

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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: Jun 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 85945 / % possible obs: 97.6 % / Redundancy: 2.9 % / CC1/2: 0.941 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.21
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.51 / Num. unique obs: 8478 / CC1/2: 0.932 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EQ7

5eq7


Resolution: 1.94→38.5 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.921 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25376 4257 5 %RANDOM
Rwork0.21174 ---
obs0.2138 81419 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.189 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å2-0.57 Å2-0.16 Å2
2--0.53 Å2-1.81 Å2
3----0.21 Å2
Refinement stepCycle: 1 / Resolution: 1.94→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7392 0 60 971 8423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0157610
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.73810377
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84751007
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.73514.903257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55615932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8321580
X-RAY DIFFRACTIONr_chiral_restr0.0970.2987
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215663
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_it2.2772.5214024
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.2993.7595014
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3022.8493586
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.21737.75211965
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 NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A71840.1
12B71840.1
21A79690.06
22C79690.06
31A71520.1
32D71520.1
41B71500.1
42C71500.1
51B73420.08
52D73420.08
61C71430.1
62D71430.1
LS refinement shellResolution: 1.944→1.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 309 -
Rwork0.299 5773 -
obs--92.98 %

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