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

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Basic information

Entry
Database: PDB / ID: 6yqd
TitleHuman histidine triad nucleotide-binding protein 2 (hHINT2) refined to 1.41 A in P212121 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: 1.407 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: 4NK0
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
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)34,4073
Polymers34,3672
Non-polymers391
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-17 kcal/mol
Surface area9800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.921, 74.113, 77.249
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: pHAT2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BX68, Hydrolases
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 8 % w/v PEG8000, 0.1 M Tris-HCl

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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: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.407→77.25 Å / Num. obs: 42522 / % possible obs: 98.8 % / Redundancy: 12.5 % / Biso Wilson estimate: 11.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.03 / Rrim(I) all: 0.079 / Χ2: 0.99 / Net I/σ(I): 18.2
Reflection shellResolution: 1.407→1.43 Å / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1560 / CC1/2: 0.755 / Rpim(I) all: 0.439 / Rrim(I) all: 0.846 / Χ2: 1.02 / % possible all: 75.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.3data scaling
MOLREP11.6.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TW2

3tw2


Resolution: 1.407→53.48 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.643 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.047
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1428 2092 4.927 %
Rwork0.1003 --
all0.102 --
obs-42457 98.673 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.947 Å2
Baniso -1Baniso -2Baniso -3
1--0.771 Å2-0 Å2-0 Å2
2--0.182 Å2-0 Å2
3---0.589 Å2
Refinement stepCycle: LAST / Resolution: 1.407→53.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1685 0 1 257 1943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0131902
X-RAY DIFFRACTIONr_bond_other_d0.0050.0171789
X-RAY DIFFRACTIONr_angle_refined_deg2.0081.6372609
X-RAY DIFFRACTIONr_angle_other_deg1.6651.5794197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2915250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08423.91897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14415334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.681159
X-RAY DIFFRACTIONr_chiral_restr0.1420.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022224
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02359
X-RAY DIFFRACTIONr_nbd_refined0.2660.2384
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.21692
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2944
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2885
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2163
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1910.27
X-RAY DIFFRACTIONr_nbd_other0.1890.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1090.212
X-RAY DIFFRACTIONr_mcbond_it1.9881.478952
X-RAY DIFFRACTIONr_mcbond_other1.9891.477950
X-RAY DIFFRACTIONr_mcangle_it2.4632.2281218
X-RAY DIFFRACTIONr_mcangle_other2.4632.2281218
X-RAY DIFFRACTIONr_scbond_it5.211.895950
X-RAY DIFFRACTIONr_scbond_other5.211.895950
X-RAY DIFFRACTIONr_scangle_it5.6032.7041391
X-RAY DIFFRACTIONr_scangle_other5.6022.7031391
X-RAY DIFFRACTIONr_lrange_it5.21920.7022197
X-RAY DIFFRACTIONr_lrange_other4.38419.342129
X-RAY DIFFRACTIONr_rigid_bond_restr5.32533691
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
1.407-1.4440.221400.17624420.17831120.9250.93282.96920.147
1.444-1.4830.1781550.11828820.12130540.9580.96799.44340.098
1.483-1.5260.171400.128270.10329690.9560.97499.93260.083
1.526-1.5730.1481520.08727480.0929030.9720.98199.89670.071
1.573-1.6250.1261370.07926640.08228020.9790.98499.96430.066
1.625-1.6820.1321360.07625800.07927160.9750.9851000.063
1.682-1.7450.1361340.07424790.07726130.9760.9861000.063
1.745-1.8160.1341270.0724110.07325390.9770.98899.96060.062
1.816-1.8970.1231070.07623260.07824340.9810.98799.95890.069
1.897-1.9890.1211180.07522220.07723400.9840.9881000.07
1.989-2.0970.131080.08220940.08422030.9820.98799.95460.078
2.097-2.2240.1241090.07920120.08121210.9830.9891000.078
2.224-2.3770.119950.07518870.07719820.9850.991000.075
2.377-2.5670.137990.0917430.09218430.980.98799.94570.092
2.567-2.8120.139810.10316220.10517030.9780.9831000.109
2.812-3.1420.183770.1115020.11415790.970.9811000.119
3.142-3.6260.132650.1113250.11113900.9820.9841000.121
3.626-4.4360.144630.11211240.11411870.9760.9851000.131
4.436-6.2520.123300.1269270.1269570.9860.9851000.15
6.252-53.480.251190.1975480.1985690.9590.96399.64850.235

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