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

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Basic information

Entry
Database: PDB / ID: 6ypx
TitleHuman histidine triad nucleotide-binding protein 2 (hHINT2) refined to 2.11 A in C2221 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
CACODYLATE ION / Adenosine 5'-monophosphoramidase HINT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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: 4NJZ
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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
CCC: Histidine triad nucleotide-binding protein 2, mitochondrial
DDD: Histidine triad nucleotide-binding protein 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,23910
Polymers68,7354
Non-polymers5046
Water12,142674
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)34,5974
Polymers34,3672
Non-polymers2292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-13 kcal/mol
Surface area9690 Å2
MethodPISA
2
CCC: Histidine triad nucleotide-binding protein 2, mitochondrial
DDD: Histidine triad nucleotide-binding protein 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6436
Polymers34,3672
Non-polymers2754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-24 kcal/mol
Surface area9780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.411, 153.992, 74.785
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11AAA-350-

HOH

21AAA-449-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains AAA BBB
22Chains AAA CCC
33Chains AAA DDD
44Chains BBB CCC
55Chains BBB DDD
66Chains CCC DDD

NCS ensembles :
IDDetails
6Chains CCC DDD
1Chains AAA BBB
2Chains AAA CCC
3Chains AAA DDD
4Chains BBB CCC
5Chains BBB DDD

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


Mass: 136.989 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6AsO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 674 / 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: 3.99 Å3/Da / Density % sol: 69.15 % / Description: rectangular plates
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium citrate, 0.1 M sodium cacodylate, 30 % 2-propanol

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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: 0.9669 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9669 Å / Relative weight: 1
ReflectionResolution: 2.11→102.94 Å / Num. obs: 46164 / % possible obs: 99.6 % / Redundancy: 12.2 % / Biso Wilson estimate: 15.482 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.094 / Rrim(I) all: 0.24 / Χ2: 1 / Net I/σ(I): 11.3
Reflection shellResolution: 2.11→2.17 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.041 / Mean I/σ(I) obs: 2 / Num. unique obs: 3623 / CC1/2: 0.697 / Rpim(I) all: 0.568 / Rrim(I) all: 1.194 / Χ2: 0.96 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
MOLREP11.2.05phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TW2
Resolution: 2.11→102.94 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.712 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.125
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1845 2349 5.091 %
Rwork0.1476 --
all0.149 --
obs-46144 99.59 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.345 Å2
Baniso -1Baniso -2Baniso -3
1-0.105 Å20 Å2-0 Å2
2--1.922 Å20 Å2
3----2.027 Å2
Refinement stepCycle: LAST / Resolution: 2.11→102.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3532 0 24 674 4230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133755
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173572
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.645123
X-RAY DIFFRACTIONr_angle_other_deg1.4071.5798326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5925473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.52823.228189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28515633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9161520
X-RAY DIFFRACTIONr_chiral_restr0.0880.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024243
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02709
X-RAY DIFFRACTIONr_nbd_refined0.2290.2800
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.23465
X-RAY DIFFRACTIONr_nbtor_refined0.1580.21872
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21820
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2509
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1360.29
X-RAY DIFFRACTIONr_nbd_other0.2070.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2010.226
X-RAY DIFFRACTIONr_mcbond_it2.0212.3621868
X-RAY DIFFRACTIONr_mcbond_other2.0182.3611866
X-RAY DIFFRACTIONr_mcangle_it2.9883.5312349
X-RAY DIFFRACTIONr_mcangle_other2.9883.5312349
X-RAY DIFFRACTIONr_scbond_it3.2422.6491887
X-RAY DIFFRACTIONr_scbond_other3.2422.6511888
X-RAY DIFFRACTIONr_scangle_it4.9363.8642774
X-RAY DIFFRACTIONr_scangle_other4.9353.8662775
X-RAY DIFFRACTIONr_lrange_it7.57531.5544492
X-RAY DIFFRACTIONr_lrange_other7.25629.9874268
X-RAY DIFFRACTIONr_ncsr_local_group_10.0920.053545
X-RAY DIFFRACTIONr_ncsr_local_group_20.0810.053539
X-RAY DIFFRACTIONr_ncsr_local_group_30.0850.053567
X-RAY DIFFRACTIONr_ncsr_local_group_40.0710.053583
X-RAY DIFFRACTIONr_ncsr_local_group_50.0830.053536
X-RAY DIFFRACTIONr_ncsr_local_group_60.0860.053534
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
2.11-2.1650.2711770.2530870.25133940.8360.83696.16970.229
2.165-2.2240.2481750.21430610.21632790.8770.89598.68860.19
2.224-2.2890.2341570.19530470.19732110.8970.91699.7820.167
2.289-2.3590.21610.16729660.16831270.9320.941000.142
2.359-2.4360.2011290.17128790.17230080.9310.9421000.142
2.436-2.5220.2121420.16128180.16429610.9270.94499.96620.135
2.522-2.6170.2241690.16326510.16728200.9290.9461000.134
2.617-2.7240.2351300.15926110.16227420.9340.95399.96350.131
2.724-2.8450.1931260.14924810.15126070.9470.961000.125
2.845-2.9830.1771370.14523770.14725140.9590.9651000.122
2.983-3.1450.2021210.14622710.14923920.9480.9631000.125
3.145-3.3350.1651060.13221570.13422630.9620.9721000.118
3.335-3.5650.151140.1220340.12121490.9740.9899.95350.11
3.565-3.850.1471110.11518780.11619890.9740.9811000.107
3.85-4.2170.14930.10417340.10618280.9770.98399.94530.098
4.217-4.7140.141840.10116010.10316850.9790.9851000.096
4.714-5.4420.126770.11114060.11214840.9840.98599.93260.105
5.442-6.660.153660.14112040.14112700.9770.9751000.13
6.66-9.3990.201500.1429620.14510120.9610.9791000.136
9.399-102.940.253240.2255700.2275980.9310.94799.33110.228

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