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- PDB-6yvp: Human histidine triad nucleotide-binding protein 2 (hHINT2) compl... -

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Basic information

Entry
Database: PDB / ID: 6yvp
TitleHuman histidine triad nucleotide-binding protein 2 (hHINT2) complexed with dGMP and refined to 2.77 A
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
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / Adenosine 5'-monophosphoramidase HINT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsDolot, R.D. / Krakowiak, A. / Nawrot, B.C.
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 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0624
Polymers34,3672
Non-polymers6942
Water2,126118
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)35,0624
Polymers34,3672
Non-polymers6942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5480 Å2
ΔGint-22 kcal/mol
Surface area9570 Å2
MethodPISA
2
BBB: Histidine triad nucleotide-binding protein 2, mitochondrial
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)35,0624
Polymers34,3672
Non-polymers6942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5540 Å2
ΔGint-23 kcal/mol
Surface area9510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.649, 36.531, 86.887
Angle α, β, γ (deg.)90.000, 103.034, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

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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.: 2
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-DGP / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / Deoxyguanosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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

CrystalDescription: Needles
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / Details: 15 % (w/v) PEG6000, 5 % (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.77→42.32 Å / Num. obs: 5698 / % possible obs: 99.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 31.4 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.176 / Rrim(I) all: 0.266 / Χ2: 0.95 / Net I/σ(I): 5.5
Reflection shellResolution: 2.77→2.92 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 2 / Num. unique obs: 814 / CC1/2: 0.799 / Rpim(I) all: 0.589 / Rrim(I) all: 0.894 / Χ2: 0.94 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
MOLREP11.7.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YQD:B

6yqd


Resolution: 2.77→42.32 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.862 / SU B: 24.159 / SU ML: 0.45 / Cross valid method: THROUGHOUT / ESU R Free: 0.544
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3077 565 9.921 %
Rwork0.2077 --
all0.218 --
obs-5695 98.649 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.978 Å2
Baniso -1Baniso -2Baniso -3
1--1.837 Å20 Å21.086 Å2
2--5.134 Å20 Å2
3----3.431 Å2
Refinement stepCycle: LAST / Resolution: 2.77→42.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 46 118 1920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131858
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171757
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.6782536
X-RAY DIFFRACTIONr_angle_other_deg1.1391.5944090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4865224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.66122.88990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.37315308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2691510
X-RAY DIFFRACTIONr_chiral_restr0.0650.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022044
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02354
X-RAY DIFFRACTIONr_nbd_refined0.1960.2373
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.21692
X-RAY DIFFRACTIONr_nbtor_refined0.1530.2855
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2859
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.248
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1370.213
X-RAY DIFFRACTIONr_nbd_other0.1690.2110
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.190.210
X-RAY DIFFRACTIONr_mcbond_it1.5763.772898
X-RAY DIFFRACTIONr_mcbond_other1.5773.771896
X-RAY DIFFRACTIONr_mcangle_it2.685.6511121
X-RAY DIFFRACTIONr_mcangle_other2.6795.6521121
X-RAY DIFFRACTIONr_scbond_it1.3763.907959
X-RAY DIFFRACTIONr_scbond_other1.3733.906955
X-RAY DIFFRACTIONr_scangle_it2.4095.8151414
X-RAY DIFFRACTIONr_scangle_other2.4115.8131409
X-RAY DIFFRACTIONr_lrange_it4.97543.2081983
X-RAY DIFFRACTIONr_lrange_other4.97343.2261982
X-RAY DIFFRACTIONr_ncsr_local_group_10.1260.053228
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
2.77-2.8420.473390.3573870.3684310.6040.63198.83990.342
2.842-2.9190.535330.3243530.343920.6070.7298.46940.305
2.919-3.0030.399400.2833580.2944050.7510.76598.27160.265
3.003-3.0950.383390.2663490.2773940.7260.80498.47720.247
3.095-3.1960.373370.2393050.2543490.7950.84497.99430.22
3.196-3.3080.318420.2093400.2213850.8450.87599.22080.193
3.308-3.4320.26230.2093150.2133400.8760.89899.41180.196
3.432-3.5710.348340.1982920.2123310.8590.91398.48940.191
3.571-3.7290.329300.1892890.23220.8570.9399.06830.186
3.729-3.9090.241340.1662810.1753190.9280.94598.74610.157
3.909-4.1190.282270.1722740.1823060.8910.93398.3660.165
4.119-4.3660.291290.1812480.1942780.90.92799.64030.17
4.366-4.6640.16260.1732390.1722690.9310.92798.5130.167
4.664-5.0320.251260.1672200.1772510.9550.93698.0080.158
5.032-5.5050.327210.2162010.2262240.8390.91199.10710.203
5.505-6.1420.411280.181820.2092150.8960.93897.67440.169
6.142-7.0670.336190.1991600.2111810.9290.93498.8950.189
7.067-8.5950.192170.1381460.1431630.9490.9721000.138
8.595-11.9130.141100.1561210.1551320.9810.9799.24240.16
11.913-42.3240.39110.319690.328840.9090.92195.23810.353

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