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- PDB-6yi0: Human histidine triad nucleotide-binding protein 2 (hHINT2) refin... -

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Basic information

Entry
Database: PDB / ID: 6yi0
TitleHuman histidine triad nucleotide-binding protein 2 (hHINT2) refined to 1.65 A in P41212 space group
ComponentsHistidine triad nucleotide-binding protein 2, mitochondrial
KeywordsHYDROLASE / Nucleotide binding protein
Function / homology
Function and homology information


Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / steroid biosynthetic process / RHOD GTPase cycle / lipid catabolic process / mitochondrial outer membrane / hydrolase activity / mitochondrial matrix / nucleotide binding / apoptotic process ...Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / steroid biosynthetic process / RHOD GTPase cycle / lipid catabolic process / mitochondrial outer membrane / hydrolase activity / mitochondrial matrix / nucleotide binding / apoptotic process / mitochondrion / cytoplasm
Similarity search - Function
Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like superfamily
Similarity search - Domain/homology
Adenosine 5'-monophosphoramidase HINT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsDolot, R.D. / Wlodarczyk, A. / Bujacz, G.D. / Nawrot, B.C.
Funding support Poland, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher Education (Poland)N N204 516139 Poland
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2021
Title: Biochemical, crystallographic and biophysical characterization of histidine triad nucleotide-binding protein 2 with different ligands including a non-hydrolyzable analog of Ap4A.
Authors: Dolot, R. / Krakowiak, A. / Kaczmarek, R. / Wlodarczyk, A. / Pichlak, M. / Nawrot, B.
History
DepositionMar 31, 2020Deposition site: PDBE / Processing site: PDBE
SupersessionApr 29, 2020ID: 4NJX
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry
Revision 1.2Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Histidine triad nucleotide-binding protein 2, mitochondrial
BBB: Histidine triad nucleotide-binding protein 2, mitochondrial
DDD: Histidine triad nucleotide-binding protein 2, mitochondrial
CCC: Histidine triad nucleotide-binding protein 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7585
Polymers68,7354
Non-polymers231
Water6,864381
1
AAA: Histidine triad nucleotide-binding protein 2, mitochondrial
BBB: Histidine triad nucleotide-binding protein 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3903
Polymers34,3672
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-20 kcal/mol
Surface area9570 Å2
MethodPISA
2
DDD: Histidine triad nucleotide-binding protein 2, mitochondrial
CCC: Histidine triad nucleotide-binding protein 2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)34,3672
Polymers34,3672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-15 kcal/mol
Surface area9250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.945, 76.945, 140.454
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Histidine triad nucleotide-binding protein 2, mitochondrial / HINT-2 / HINT-3 / HIT-17kDa / PKCI-1-related HIT protein


Mass: 17183.725 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HINT2 / Plasmid: pGAT2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BX68, Hydrolases
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% (v/v) ethylene glycol, 5% (w/v) PEG 3350, 20 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.65→46.82 Å / Num. obs: 51576 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 19.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.035 / Rrim(I) all: 0.084 / Χ2: 0.99 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.68111.0822.125050.820.4961.1910.96100
9.04-46.827.70.0436.23850.9990.0190.0440.9297.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless1.11.21data scaling
MOLREP11.7.01phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TW2

3tw2


Resolution: 1.65→43.044 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.225 / WRfactor Rwork: 0.177 / SU B: 2.996 / SU ML: 0.096 / Average fsc free: 0.8628 / Average fsc work: 0.8764 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.109
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2331 2608 5.065 %
Rwork0.1845 48882 -
all0.187 --
obs-51490 99.957 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.062 Å2
Baniso -1Baniso -2Baniso -3
1--1.569 Å20 Å20 Å2
2---1.569 Å20 Å2
3---3.138 Å2
Refinement stepCycle: LAST / Resolution: 1.65→43.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 1 381 3690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133518
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173318
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.6364808
X-RAY DIFFRACTIONr_angle_other_deg1.331.5747744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1895447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03623.444180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4115591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1571518
X-RAY DIFFRACTIONr_chiral_restr0.0840.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024021
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02665
X-RAY DIFFRACTIONr_nbd_refined0.20.2730
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.23185
X-RAY DIFFRACTIONr_nbtor_refined0.1540.21703
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21497
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0670.21
X-RAY DIFFRACTIONr_metal_ion_refined0.3530.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2570.211
X-RAY DIFFRACTIONr_nbd_other0.2260.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.224
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2420.21
X-RAY DIFFRACTIONr_mcbond_it2.7573.3631758
X-RAY DIFFRACTIONr_mcbond_other2.7583.3621756
X-RAY DIFFRACTIONr_mcangle_it3.7035.0252215
X-RAY DIFFRACTIONr_mcangle_other3.7035.0252215
X-RAY DIFFRACTIONr_scbond_it2.9473.61760
X-RAY DIFFRACTIONr_scbond_other2.9473.61760
X-RAY DIFFRACTIONr_scangle_it4.3875.2992593
X-RAY DIFFRACTIONr_scangle_other4.3875.2992593
X-RAY DIFFRACTIONr_lrange_it6.11240.8263959
X-RAY DIFFRACTIONr_lrange_other6.02240.4433877
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.65-1.6930.3532120.32535320.32637440.4810.5221000.288
1.693-1.7390.2831960.29734290.29636250.7480.6981000.261
1.739-1.7890.2671900.2633860.2635760.8440.8161000.221
1.789-1.8440.2811730.24732620.24834370.8340.84699.94180.211
1.844-1.9050.2421540.21931920.2233460.8880.8941000.189
1.905-1.9720.2371660.20530820.20632480.9150.9191000.177
1.972-2.0460.2871710.20629490.2131200.8850.921000.183
2.046-2.1290.2761290.20329070.20630360.8930.9251000.178
2.129-2.2240.2141470.18527560.18629030.9370.941000.165
2.224-2.3320.2331320.17926530.18227850.9250.9431000.163
2.332-2.4570.2281420.17625120.17926540.9280.9421000.159
2.457-2.6060.2211430.18223800.18425230.930.9381000.168
2.606-2.7850.2391260.17322510.17623770.9350.9491000.163
2.785-3.0070.2341120.16221090.16522210.9440.9581000.155
3.007-3.2930.245750.16919830.17220580.9310.9561000.167
3.293-3.6790.212920.17317830.17518750.9530.9541000.18
3.679-4.2430.253830.1715950.17416780.9370.9561000.186
4.243-5.1840.172760.13913740.14114500.9650.9751000.161
5.184-7.2780.216550.17810840.1811390.9560.9621000.195
7.278-43.0440.205340.186640.1817140.960.96997.75910.22

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