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

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Basic information

Entry
Database: PDB / ID: 6ypr
TitleHuman histidine triad nucleotide-binding protein 2 (hHINT2) refined to 1.26 A in H32 space group
ComponentsHistidine triad nucleotide-binding protein 2, mitochondrial
KeywordsHYDROLASE / Nucleotide binding protein
Function / homology
Function and homology information


negative regulation of peptidyl-lysine acetylation / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / steroid biosynthetic process / RHOD GTPase cycle / lipid catabolic process / mitochondrial outer membrane / hydrolase activity / nucleotide binding / apoptotic process ...negative regulation of peptidyl-lysine acetylation / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / steroid biosynthetic process / RHOD GTPase cycle / lipid catabolic process / mitochondrial outer membrane / hydrolase activity / 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: 1.26 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
DepositionApr 16, 2020Deposition site: PDBE / Processing site: PDBE
SupersessionApr 29, 2020ID: 4NJY
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
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
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)17,4604
Polymers17,1841
Non-polymers2763
Water1,51384
1
AAA: Histidine triad nucleotide-binding protein 2, mitochondrial
hetero molecules

AAA: Histidine triad nucleotide-binding protein 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9208
Polymers34,3672
Non-polymers5536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area5270 Å2
ΔGint-25 kcal/mol
Surface area8430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.076, 72.076, 103.576
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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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.: 1
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.8 M Na/K Tartrate, 0.1 M HEPES 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.26→36.043 Å / Num. obs: 28102 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 9.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.043 / Rrim(I) all: 0.073 / Χ2: 1.02 / Net I/σ(I): 12.6
Reflection shellResolution: 1.26→1.28 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2 / Num. unique obs: 1352 / CC1/2: 0.685 / Rpim(I) all: 0.492 / Rrim(I) all: 0.815 / Χ2: 1.03 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.5.27data scaling
MOLREP11.4.06phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TW2

3tw2


Resolution: 1.26→36.043 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.494 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.035
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1427 1375 4.893 %
Rwork0.1171 --
all0.118 --
obs-28101 99.73 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.669 Å2
Baniso -1Baniso -2Baniso -3
1--0.665 Å2-0.333 Å20 Å2
2---0.665 Å20 Å2
3---2.159 Å2
Refinement stepCycle: LAST / Resolution: 1.26→36.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms756 0 18 84 858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.013918
X-RAY DIFFRACTIONr_bond_other_d0.010.017867
X-RAY DIFFRACTIONr_angle_refined_deg2.0771.6371259
X-RAY DIFFRACTIONr_angle_other_deg1.6111.5762035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.335119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.90823.91346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.13115154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.379154
X-RAY DIFFRACTIONr_chiral_restr0.1410.2107
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021065
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02171
X-RAY DIFFRACTIONr_nbd_refined0.2110.2180
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2080.2806
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2444
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.2422
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0150.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.9060.214
X-RAY DIFFRACTIONr_nbd_other0.1620.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4030.216
X-RAY DIFFRACTIONr_mcbond_it1.3421.019443
X-RAY DIFFRACTIONr_mcbond_other1.3451.018441
X-RAY DIFFRACTIONr_mcangle_it1.681.54573
X-RAY DIFFRACTIONr_mcangle_other1.6791.54573
X-RAY DIFFRACTIONr_scbond_it3.3541.551472
X-RAY DIFFRACTIONr_scbond_other3.3511.553473
X-RAY DIFFRACTIONr_scangle_it3.8562.154684
X-RAY DIFFRACTIONr_scangle_other3.8542.158685
X-RAY DIFFRACTIONr_lrange_it4.60914.781012
X-RAY DIFFRACTIONr_lrange_other3.81613.969993
X-RAY DIFFRACTIONr_rigid_bond_restr10.47931781
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
1.26-1.2930.2521150.2319180.23120380.9080.88299.75470.211
1.293-1.3280.226980.20919130.2120180.9180.91899.65310.186
1.328-1.3670.202990.18518460.18519520.9180.93499.64140.161
1.367-1.4090.195990.16717840.16818870.9360.9599.7880.14
1.409-1.4550.168930.14917460.1518430.9740.95999.7830.125
1.455-1.5060.166920.1316980.13217930.9520.96499.83270.108
1.506-1.5620.144790.11416390.11517210.9670.97699.82570.096
1.562-1.6260.125810.115650.10116470.9810.98399.93930.086
1.626-1.6980.126840.09315170.09516020.980.98499.93760.08
1.698-1.7810.125790.08514430.08715240.9810.98899.86880.076
1.781-1.8770.12710.08413850.08614570.9850.98999.93140.077
1.877-1.990.11600.07713210.07813870.9880.9999.56740.072
1.99-2.1270.112700.08712130.08812870.9840.98799.68920.085
2.127-2.2970.125410.0911690.09112110.9840.98799.91740.09
2.297-2.5150.125450.09410780.09511230.9830.9881000.097
2.515-2.8110.121430.1019690.10210150.9810.98699.70440.106
2.811-3.2420.142590.1178480.1199100.9740.97999.67030.131
3.242-3.9630.148330.1137340.1147750.9780.98398.96770.133
3.963-5.5710.12180.1315900.1316120.9850.98499.34640.162
5.571-36.0430.171160.2043500.2023720.9870.96798.38710.244

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