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- PDB-4zkl: Crystal structure of human histidine triad nucleotide-binding pro... -

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Basic information

Entry
Database: PDB / ID: 4zkl
TitleCrystal structure of human histidine triad nucleotide-binding protein 1 (hHINT1) complexed with JB419 (AP4A analog)
ComponentsHistidine triad nucleotide-binding protein 1
KeywordsHYDROLASE / HINT / HIT / Phosphoramidase / Complex / AP4A analog
Function / homology
Function and homology information


purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of calcium-mediated signaling ...purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of calcium-mediated signaling / protein kinase C binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cytoskeleton / hydrolase activity / nucleotide binding / regulation of DNA-templated transcription / signal transduction / proteolysis / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / 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 / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Chem-JB6 / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsDolot, R.M. / Kaczmarek, R. / Seda, A. / Krakowiak, A. / Baraniak, J. / Nawrot, B.
CitationJournal: Int.J.Biol.Macromol. / Year: 2016
Title: Crystallographic studies of the complex of human HINT1 protein with a non-hydrolyzable analog of Ap4A.
Authors: Dolot, R. / Kaczmarek, R. / Seda, A. / Krakowiak, A. / Baraniak, J. / Nawrot, B.
History
DepositionApr 30, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine triad nucleotide-binding protein 1
B: Histidine triad nucleotide-binding protein 1
C: Histidine triad nucleotide-binding protein 1
D: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7877
Polymers55,2964
Non-polymers1,4913
Water3,495194
1
A: Histidine triad nucleotide-binding protein 1
B: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7924
Polymers27,6482
Non-polymers1,1442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-21 kcal/mol
Surface area9910 Å2
MethodPISA
2
C: Histidine triad nucleotide-binding protein 1
D: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9953
Polymers27,6482
Non-polymers3471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-21 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.714, 46.419, 103.413
Angle α, β, γ (deg.)90.00, 97.41, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA15 - 12515 - 125
21PROPROBB15 - 12515 - 125
12GLYGLYAA15 - 12615 - 126
22GLYGLYCC15 - 12615 - 126
13PROPROAA15 - 12515 - 125
23PROPRODD15 - 12515 - 125
14PROPROBB15 - 12515 - 125
24PROPROCC15 - 12515 - 125
15PROPROBB14 - 12514 - 125
25PROPRODD14 - 12514 - 125
16PROPROCC15 - 12515 - 125
26PROPRODD15 - 12515 - 125

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Histidine triad nucleotide-binding protein 1 / Adenosine 5'-monophosphoramidase / Protein kinase C inhibitor 1 / Protein kinase C-interacting ...Adenosine 5'-monophosphoramidase / Protein kinase C inhibitor 1 / Protein kinase C-interacting protein 1 / PKCI-1


Mass: 13823.931 Da / Num. of mol.: 4 / Fragment: UNP residues 1-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HINT1, HINT, PKCI1, PRKCNH1 / Plasmid: pSGA02 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49773, Hydrolases
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-JB6 / (2R,3R,4S,5R)-2-(6-aminopurin-9-yl)-5-[2-[[(2S)-3-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl]oxy-2-oxidanyl-propoxy]-sulfanyl-phosphoryl]oxyethyl]oxolane-3,4-diol


Mass: 796.663 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H34N10O13P2S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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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: 3.03 Å3/Da / Density % sol: 59.45 % / Description: plates
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 19% w/v PEG4000, 0.1 M sodium cacodylate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9669 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2013
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9669 Å / Relative weight: 1
ReflectionResolution: 2.34→102.55 Å / Num. obs: 25059 / % possible obs: 97.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 7.1
Reflection shellResolution: 2.34→2.42 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 1.6 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TW2

3tw2


Resolution: 2.34→102.55 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.944 / SU B: 21.98 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23907 1222 4.9 %RANDOM
Rwork0.18642 ---
obs0.189 23826 97.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.124 Å2
Baniso -1Baniso -2Baniso -3
1-3.12 Å2-0 Å20.19 Å2
2---4.22 Å2-0 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.34→102.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 97 194 3786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0193705
X-RAY DIFFRACTIONr_bond_other_d0.0130.023537
X-RAY DIFFRACTIONr_angle_refined_deg2.1621.9845018
X-RAY DIFFRACTIONr_angle_other_deg1.91738176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8995451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.92424.013157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1215624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6231517
X-RAY DIFFRACTIONr_chiral_restr0.1350.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214095
X-RAY DIFFRACTIONr_gen_planes_other0.010.02830
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3922.6541810
X-RAY DIFFRACTIONr_mcbond_other2.3922.6531809
X-RAY DIFFRACTIONr_mcangle_it4.0883.9632259
X-RAY DIFFRACTIONr_mcangle_other4.0873.9642260
X-RAY DIFFRACTIONr_scbond_it2.5673.0251895
X-RAY DIFFRACTIONr_scbond_other2.5673.0251895
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.334.462760
X-RAY DIFFRACTIONr_long_range_B_refined9.23422.5084133
X-RAY DIFFRACTIONr_long_range_B_other9.23322.524134
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A127980.08
12B127980.08
21A131280.07
22C131280.07
31A126280.1
32D126280.1
41B128000.08
42C128000.08
51B127240.11
52D127240.11
61C127180.09
62D127180.09
LS refinement shellResolution: 2.34→2.401 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 89 -
Rwork0.336 1774 -
obs--98.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5177-0.15530.42182.58030.01670.4080.0458-0.01970.1360.3373-0.05720.0710.00130.05350.01140.1131-0.00570.05140.2254-0.0250.735.5302-0.67244.1943
22.57970.765-0.03862.8175-0.17110.97030.13820.00750.00620.2403-0.0645-0.27410.02850.0361-0.07370.0833-0.0002-0.00620.2131-0.00910.727623.8975-1.23056.1359
31.3724-0.1365-0.73171.9582-1.32643.4605-0.0750.1124-0.03020.1057-0.0083-0.00020.1658-0.06560.08330.7197-0.02370.00780.0115-0.02860.368225.4825-12.484344.3633
42.3748-0.4197-0.03152.460.51233.75220.17310.1649-0.09840.08-0.1039-0.26750.1630.441-0.06920.51820.0529-0.01460.07390.01680.301535.5449-11.857128.8197
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 126
2X-RAY DIFFRACTION2B17 - 126
3X-RAY DIFFRACTION3C17 - 126
4X-RAY DIFFRACTION4D17 - 126

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