[English] 日本語
Yorodumi
- PDB-3mvt: Crystal structure of apo mADA at 2.2A resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mvt
TitleCrystal structure of apo mADA at 2.2A resolution
ComponentsAdenosine deaminase
KeywordsHYDROLASE / Adenosine Deaminase
Function / homology
Function and homology information


mature B cell apoptotic process / xanthine biosynthetic process / negative regulation of penile erection / Purine salvage / Ribavirin ADME / negative regulation of circadian sleep/wake cycle, non-REM sleep / negative regulation of mucus secretion / penile erection / purine nucleoside binding / positive regulation of germinal center formation ...mature B cell apoptotic process / xanthine biosynthetic process / negative regulation of penile erection / Purine salvage / Ribavirin ADME / negative regulation of circadian sleep/wake cycle, non-REM sleep / negative regulation of mucus secretion / penile erection / purine nucleoside binding / positive regulation of germinal center formation / negative regulation of adenosine receptor signaling pathway / cytoplasmic vesicle lumen / amide catabolic process / hypoxanthine biosynthetic process / inosine biosynthetic process / adenosine deaminase / histamine secretion / germinal center B cell differentiation / 2'-deoxyadenosine deaminase activity / hypoxanthine salvage / inhibition of non-skeletal tissue mineralization / adenosine catabolic process / deoxyadenosine catabolic process / dAMP catabolic process / adenosine deaminase activity / AMP catabolic process / adenosine metabolic process / positive regulation of T cell differentiation in thymus / dATP catabolic process / mucus secretion / negative regulation of leukocyte migration / GMP salvage / regulation of cell-cell adhesion mediated by integrin / embryonic digestive tract development / allantoin metabolic process / response to purine-containing compound / trophectodermal cell differentiation / IMP salvage / Peyer's patch development / positive regulation of smooth muscle contraction / germinal center formation / negative regulation of mature B cell apoptotic process / AMP salvage / regulation of T cell differentiation in thymus / negative regulation of thymocyte apoptotic process / anchoring junction / positive regulation of alpha-beta T cell differentiation / alpha-beta T cell differentiation / positive regulation of T cell differentiation / regulation of T cell differentiation / thymocyte apoptotic process / lung alveolus development / leukocyte migration / positive regulation of heart rate / positive regulation of T cell receptor signaling pathway / B cell proliferation / T cell differentiation / smooth muscle contraction / response to vitamin E / positive regulation of B cell proliferation / dendrite cytoplasm / positive regulation of calcium-mediated signaling / liver development / T cell activation / lung development / calcium-mediated signaling / placenta development / negative regulation of inflammatory response / positive regulation of T cell activation / T cell receptor signaling pathway / T cell differentiation in thymus / in utero embryonic development / lysosome / response to hypoxia / cell adhesion / external side of plasma membrane / neuronal cell body / negative regulation of apoptotic process / apoptotic process / extracellular space / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Adenosine deaminase / Adenosine/AMP deaminase active site / Adenosine and AMP deaminase signature. / Adenosine deaminase domain / Adenosine deaminase / Adenosine/adenine deaminase / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNiu, W. / Shu, Q. / Chen, Z. / Mathews, S. / Di Cera, E. / Frieden, C.
Citation
Journal: J.Phys.Chem.B / Year: 2010
Title: The role of Zn2+ on the structure and stability of murine adenosine deaminase.
Authors: Niu, W. / Shu, Q. / Chen, Z. / Mathews, S. / Di Cera, E. / Frieden, C.
#1: Journal: Biochemistry / Year: 1998
Title: Complexes of Adenosine Deaminase with Two Potent Inhibitors: X-ray Structures in Four Independent Molecules at pH of Maximum Activity
Authors: Wang, Z. / Quiocho, F.A.
History
DepositionMay 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Adenosine deaminase
C: Adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6505
Polymers79,4302
Non-polymers2203
Water4,774265
1
A: Adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8072
Polymers39,7151
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8433
Polymers39,7151
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.833, 93.827, 86.180
Angle α, β, γ (deg.)90.00, 96.76, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Adenosine deaminase / Adenosine aminohydrolase


Mass: 39715.188 Da / Num. of mol.: 2 / Fragment: UNP residues 4-352
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ada / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P03958, adenosine deaminase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 200 mM Ammonium sulfate, 20 % PEG 3350, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 12, 2009
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 39690 / Num. obs: 37983 / % possible obs: 95.7 % / Observed criterion σ(F): -0.6 / Observed criterion σ(I): -0.6 / Redundancy: 3.2 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 10.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1762 / % possible all: 89.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPfrom CCP4phasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1a4m

1a4m


Resolution: 2.2→33.9 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.922 / SU B: 15.401 / SU ML: 0.171 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -0.6 / σ(I): -0.6 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24494 1903 5 %RANDOM
Rwork0.18677 ---
obs0.18973 36077 95.65 %-
all-37718 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.117 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5584 0 13 265 5862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225722
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.9687742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2485696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3624.593270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.192151016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2671530
X-RAY DIFFRACTIONr_chiral_restr0.0830.2842
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214336
X-RAY DIFFRACTIONr_mcbond_it0.3531.53482
X-RAY DIFFRACTIONr_mcangle_it0.62425638
X-RAY DIFFRACTIONr_scbond_it1.28732240
X-RAY DIFFRACTIONr_scangle_it1.9034.52104
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 138 -
Rwork0.277 2466 -
obs-2466 90.2 %
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)
12.4452-1.3564-0.32666.25520.99260.65130.0760.3478-0.2277-0.9331-0.16720.3877-0.06080.00270.09120.1746-0.0119-0.0470.1193-0.02080.036677.5144-6.7593-5.5691
27.90360.5883-4.88079.68181.81334.58980.22380.657-0.1756-1.1688-0.17391.1109-0.376-0.6123-0.050.2749-0.0032-0.16680.2817-0.0830.393268.7011-16.5516-6.1714
34.6573-0.01311.79698.3461-0.15052.59970.0014-0.199-0.5210.00620.02280.26080.0187-0.0761-0.02420.08320.0105-0.00460.04980.00930.088280.4716-12.14620.252
42.576-0.02340.09176.73270.31653.4503-0.1162-0.0894-0.1928-0.08940.1311-0.47430.32330.2522-0.01490.050.00160.02280.0773-0.01510.051686.5951-6.47253.6378
50.2526-0.1856-1.015411.2897-4.62166.77040.0846-0.04550.132-0.70810.0167-0.9297-0.09830.3547-0.10130.134-0.07310.05440.28890.00540.158290.27113.5261-7.0418
62.47330.6566-0.71655.4134-1.74424.9206-0.0068-0.32290.03270.35910.0646-0.3580.13420.2319-0.05780.04340.0191-0.03390.0893-0.02020.03285.3632-0.906210.5606
711.4341-3.46490.10162.26141.82.778-0.0614-0.07940.4676-0.30370.2579-0.2931-0.49190.3686-0.19650.1079-0.04540.02250.10130.00760.108691.01525.85226.8567
82.21-2.21510.68983.73330.12773.4375-0.2499-0.4382-0.23760.91680.08690.39760.199-0.06040.1630.3532-0.06690.0860.26770.0140.051876.34341.30320.0943
92.8396-0.5550.1254.74350.55992.0593-0.0477-0.131-0.03750.0254-0.10451.11-0.0883-0.3670.15230.0304-0.00470.00930.1373-0.03550.301663.31935.11686.2122
107.9426-2.83212.29736.7098-2.11245.13480.10320.23350.4591-0.4798-0.09570.1156-0.40920.406-0.00750.1745-0.0075-0.0340.0628-0.02420.075776.359518.2118-0.2949
114.0105-1.5968-0.31154.94851.53562.13140.1060.02260.2369-0.6127-0.09910.55650.0612-0.34-0.00690.1209-0.0411-0.10650.06980.01750.143266.93517.716640.0379
127.49942.2452-0.51475.1695-0.01036.60180.08150.6948-0.8232-0.73780.06930.40630.15980.0989-0.15080.23970.0398-0.09140.1067-0.09360.205975.0274-3.712234.619
134.64040.11591.80477.6410.11452.59760.0514-0.1537-0.5339-0.03850.0470.44490.1397-0.2183-0.09840.09370.00020.00060.0808-0.00020.097372.26862.468542.0689
142.6791-1.39081.17755.1338-1.30722.77030.11420.15840.0166-0.3732-0.07430.05120.14120.0919-0.03990.0365-0.01320.00190.058-0.01390.00676.611813.041644.0923
155.11410.13432.40335.596-2.21337.3215-0.03120.085-0.14010.1109-0.1028-1.09780.38030.6120.1340.07060.0413-0.03170.1366-0.03510.242286.10156.049446.9509
162.13390.07520.06973.3271-1.27166.4028-0.0177-0.15720.10780.24180.0002-0.2331-0.12540.28380.01740.04050.0162-0.0170.1012-0.01840.024181.891615.177252.5153
174.8309-1.88983.37593.4263-2.63685.67660.054-0.8914-0.12910.82460.09540.49220.1524-0.5541-0.14940.3888-0.06030.16020.2833-0.04040.089171.723515.975963.2989
184.9594-0.3034-1.35626.74991.30187.12310.062-1.01610.51.0499-0.04170.7406-0.3583-0.7434-0.02030.24210.05330.12770.4638-0.09490.286858.914823.804461.4757
191.55770.03940.0844.36040.56721.605-0.0776-0.0790.0258-0.0393-0.0630.8781-0.0468-0.34130.14070.04180.01460.00940.1419-0.0460.206359.334719.828846.6654
209.7486-1.48942.64517.8607-1.05296.9995-0.03320.73970.5634-0.4876-0.1394-0.2355-0.37740.48820.17260.1394-0.00710.0040.09270.01650.116672.816434.390740.0384
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 40
2X-RAY DIFFRACTION2A41 - 55
3X-RAY DIFFRACTION3A56 - 85
4X-RAY DIFFRACTION4A86 - 134
5X-RAY DIFFRACTION5A135 - 143
6X-RAY DIFFRACTION6A144 - 170
7X-RAY DIFFRACTION7A171 - 179
8X-RAY DIFFRACTION8A180 - 233
9X-RAY DIFFRACTION9A234 - 322
10X-RAY DIFFRACTION10A323 - 352
11X-RAY DIFFRACTION11C4 - 22
12X-RAY DIFFRACTION12C23 - 45
13X-RAY DIFFRACTION13C46 - 88
14X-RAY DIFFRACTION14C89 - 110
15X-RAY DIFFRACTION15C111 - 142
16X-RAY DIFFRACTION16C143 - 179
17X-RAY DIFFRACTION17C180 - 237
18X-RAY DIFFRACTION18C238 - 256
19X-RAY DIFFRACTION19C257 - 336
20X-RAY DIFFRACTION20C337 - 352

+
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