[English] 日本語
Yorodumi
- PDB-3u53: Crystal structure of human Ap4A hydrolase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3u53
TitleCrystal structure of human Ap4A hydrolase
ComponentsBis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
KeywordsHYDROLASE
Function / homology
Function and homology information


bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) / bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity / AMP biosynthetic process / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / ATP biosynthetic process / nucleobase-containing compound metabolic process / Detoxification of Reactive Oxygen Species / cellular response to oxidative stress / mitochondrial matrix / apoptotic process / GTP binding
Similarity search - Function
Bis(5'-nucleosyl)-tetraphosphatase / : / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...Bis(5'-nucleosyl)-tetraphosphatase / : / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.705 Å
AuthorsGe, H.H. / Teng, M.K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Crystal structure of wild-type and mutant human Ap4A hydrolase
Authors: Ge, H.H. / Chen, X.F. / Yang, W.L. / Niu, L.W. / Teng, M.K.
History
DepositionOct 10, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
B: Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
C: Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
D: Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,41522
Polymers71,6904
Non-polymers1,72518
Water2,666148
1
A: Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3035
Polymers17,9221
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3075
Polymers17,9221
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4036
Polymers17,9221
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4036
Polymers17,9221
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.485, 72.485, 133.491
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 4 - 147 / Label seq-ID: 4 - 147

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

-
Components

#1: Protein
Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical] / asymmetrical diadenosine tetraphosphate hydrolase / Ap4A hydrolase / Ap4Aase / Nudix hydrolase


Mass: 17922.385 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT2 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P50583, bis(5'-nucleosyl)-tetraphosphatase (asymmetrical)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M Sodium citrate tribasic dihydrate, 1.2M Lithium sulfate, 0.2M Ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.705→50 Å / Num. all: 18871 / Num. obs: 17881 / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 1 / Redundancy: 7.7 % / Rmerge(I) obs: 0.0983
Reflection shellResolution: 2.705→2.775 Å / Rmerge(I) obs: 0.3756 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1312 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KT9

1kt9


Resolution: 2.705→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.883 / SU B: 31.636 / SU ML: 0.295 / Cross valid method: THROUGHOUT / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28427 969 5.1 %RANDOM
Rwork0.21297 ---
obs0.21654 17881 99.99 %-
all-18867 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.676 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20 Å20 Å2
2--1.19 Å20 Å2
3----2.39 Å2
Refinement stepCycle: LAST / Resolution: 2.705→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4539 0 91 148 4778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214710
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.9696402
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6035576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04524.629229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.27415772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9471527
X-RAY DIFFRACTIONr_chiral_restr0.1080.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213580
X-RAY DIFFRACTIONr_gen_planes_other
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_it4.111.52870
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.58724575
X-RAY DIFFRACTIONr_scbond_it4.31231840
X-RAY DIFFRACTIONr_scangle_it7.5464.51825
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1086 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.480.5
Bmedium positional0.480.5
Cmedium positional0.540.5
Dmedium positional0.520.5
Amedium thermal4.372
Bmedium thermal5.122
Cmedium thermal5.012
Dmedium thermal4.342
LS refinement shellResolution: 2.705→2.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 74 -
Rwork0.329 1312 -
obs--100 %
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)
1-1.6945-0.6812-0.62436.2614-1.7283-0.3345-0.28420.00590.019-0.14030.53170.2591-0.19310.0494-0.24750.02970.01510.04020.01650.02270.09047.001-8.8078-16.2044
22.0387-1.893-0.29771.08950.9731-0.2546-0.28370.11320.23450.35210.55610.14440.09080.2986-0.27230.06530.14810.03010.09010.1015-0.00614.4085-12.5713-12.3758
32.3263-5.49815.33253.5531-6.70516.3804-0.4782-0.05450.47310.08570.0287-0.7732-0.27190.16720.44950.0894-0.0272-0.02630.07420.00240.094916.43080.965-21.6007
4-0.0415-0.9548-0.19621.4124-0.63340.841-0.0024-0.0032-0.0174-0.03340.020.1108-0.0730.0088-0.01760.0509-0.0147-0.00140.04820.01160.06237.3125-1.2764-21.5601
51.70580.3154-0.62421.13340.55320.2319-0.1159-0.19320.00110.13740.11790.03160.10080.1703-0.00210.04230.07710.00960.06070.018-0.001912.3307-6.2199-12.4052
62.4058-0.4609-1.0038-1.1976-0.78931.17850.2240.10920.13810.0388-0.21550.07260.2544-0.0706-0.00850.07080.0540.06740.01360.02530.035947.241125.4745-2.3916
72.218629.3745-1.808910.3136-29.56723.4754-3.0077-1.2847-2.0545-4.15281.5185-0.23613.1548-1.73561.48910.893-0.12230.320.1280.09710.463138.53911.8233-0.0807
81.7119-0.4203-0.71270.0254-0.34891.15820.0359-0.12750.0818-0.0507-0.0375-0.01690.0568-0.01890.00160.0638-0.01580.00480.056-0.0140.028637.581629.95358.289
91.0945-0.56460.02480.339-0.16140.90660.2081-0.00930.0157-0.0994-0.14610.04070.0610.0026-0.06210.05140.0182-0.00050.0252-0.00260.034340.830522.31611.1134
100.98843.17051.54625.06880.0030.68330.20180.1982-0.0765-0.087-0.139-0.00270.08490.0402-0.06280.04250.07580.03080.0520.0680.046238.984629.8347-9.3444
110.7655-0.0373-0.62350.7173-0.1303-0.32540.0530.1073-0.0745-0.0410.032-0.2214-0.139-0.0321-0.0850.0859-0.0479-0.03790.01550.0010.104247.158249.369520.909
123.32153.04572.25771.59163.45470.3971-0.28320.10610.1333-0.2581-0.05220.3412-0.17870.10240.33540.1292-0.0402-0.04860.0506-0.007-0.014735.719850.898710.3274
132.4350.01980.474-0.15421.0641-0.23970.19640.0779-0.175-0.2108-0.13330.0452-0.1542-0.2387-0.06320.10920.03850.03650.05060.00230.023332.870745.97718.1557
141.389-2.0656-0.0879-1.13660.6627-0.3797-0.31970.029-0.2592-0.03730.2923-0.30670.23740.0090.02750.0484-0.04460.0804-0.004-0.03370.074349.014246.417713.9445
151.75130.26710.8661.9614-1.1041-0.9025-0.0082-0.21430.1425-0.02250.03380.0890.0326-0.0138-0.02570.0948-0.03560.00350.0178-0.03510.00741.689150.812523.2835
162.3451.0681-0.4320.40230.8097-0.5208-0.0972-0.0934-0.0808-0.03320.05470.1902-0.22530.02610.04250.10090.0447-0.05170.00750.00780.0799-11.143113.0668-4.0185
172.5933-1.82850.59511.2277-2.46710.2019-0.3519-0.2720.04120.07610.1809-0.2937-0.2416-0.22020.1710.11520.0386-0.04530.0783-0.0102-0.00820.502914.64836.7663
18-0.1178-0.47990.6066-0.0449-0.87270.18950.2025-0.1019-0.1923-0.0368-0.08840.0455-0.03360.1506-0.11410.0547-0.00680.01540.0321-0.01150.05361.30178.8802-0.8711
190.8288-1.878-0.25052.66190.2672-1.33620.03640.01230.3718-0.06190.1827-0.07950.01640.0024-0.21910.04130.029-0.00650.03720.01250.0217-7.562119.1265-2.5329
200.5571-0.6122-0.61643.0829-0.1198-0.20550.32310.3311-0.05160.0944-0.3057-0.0301-0.1684-0.0592-0.01740.03480.0729-0.01940.0416-0.02520.0271-6.07074.6361-10.8115
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 16
2X-RAY DIFFRACTION2A17 - 34
3X-RAY DIFFRACTION3A35 - 46
4X-RAY DIFFRACTION4A47 - 102
5X-RAY DIFFRACTION5A103 - 147
6X-RAY DIFFRACTION6B4 - 33
7X-RAY DIFFRACTION7B34 - 38
8X-RAY DIFFRACTION8B39 - 78
9X-RAY DIFFRACTION9B79 - 126
10X-RAY DIFFRACTION10B127 - 147
11X-RAY DIFFRACTION11C4 - 32
12X-RAY DIFFRACTION12C33 - 66
13X-RAY DIFFRACTION13C67 - 93
14X-RAY DIFFRACTION14C94 - 105
15X-RAY DIFFRACTION15C106 - 147
16X-RAY DIFFRACTION16D4 - 32
17X-RAY DIFFRACTION17D33 - 67
18X-RAY DIFFRACTION18D68 - 99
19X-RAY DIFFRACTION19D100 - 131
20X-RAY DIFFRACTION20D132 - 147

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more