[English] 日本語
Yorodumi
- PDB-3uaz: Crystal structure of Bacillus cereus adenosine phosphorylase D204... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uaz
TitleCrystal structure of Bacillus cereus adenosine phosphorylase D204N mutant complexed with inosine
ComponentsPurine nucleoside phosphorylase deoD-type
KeywordsTRANSFERASE / Necleoside phosphorylase I (NP-I) family
Function / homology
Function and homology information


purine nucleoside metabolic process / nucleoside catabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity
Similarity search - Function
Purine nucleoside phosphorylase DeoD-type / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
INOSINE / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsDessanti, P. / Zhang, Y. / Allegrini, S. / Tozzi, M.G. / Sgarrella, F. / Ealick, S.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural basis of the substrate specificity of Bacillus cereus adenosine phosphorylase.
Authors: Dessanti, P. / Zhang, Y. / Allegrini, S. / Tozzi, M.G. / Sgarrella, F. / Ealick, S.E.
History
DepositionOct 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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: Purine nucleoside phosphorylase deoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2485
Polymers25,6991
Non-polymers5484
Water3,513195
1
A: Purine nucleoside phosphorylase deoD-type
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)157,48730
Polymers154,1966
Non-polymers3,29124
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_666-y+1,-x+1,-z+3/21
crystal symmetry operation11_656-x+y+1,y,-z+3/21
crystal symmetry operation12_556x,x-y,-z+3/21
Buried area28310 Å2
ΔGint-276 kcal/mol
Surface area42090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.700, 122.700, 68.000
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-429-

HOH

21A-431-

HOH

31A-433-

HOH

41A-434-

HOH

-
Components

#1: Protein Purine nucleoside phosphorylase deoD-type / PNP


Mass: 25699.389 Da / Num. of mol.: 1 / Fragment: Adenosine phosphorylase / Mutation: D204N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: deoD / Plasmid: pET5b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5EEL8, purine-nucleoside phosphorylase
#2: Chemical ChemComp-NOS / INOSINE / Inosine


Mass: 268.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N4O5
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.87 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.1 - 1.25 M sodium citrate, pH 5.5, vapor diffusion, hanging drop, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. all: 59410 / Num. obs: 59410 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.077 / Χ2: 1.97 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.4-1.4580.52658581.4561100
1.45-1.518.20.38558771.6111100
1.51-1.588.20.29758701.7971100
1.58-1.668.30.23258641.9521100
1.66-1.768.30.18758872.2431100
1.76-1.98.30.14559172.3411100
1.9-2.098.30.11659412.4041100
2.09-2.398.20.10159782.581100
2.39-3.018.10.06860421.7781100
3.01-207.80.03861761.483197.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ECP

1ecp


Resolution: 1.4→19.812 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9355 / SU ML: 0.26 / σ(F): 1 / Phase error: 12.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1547 2833 4.94 %RANDOM
Rwork0.1403 ---
obs0.141 57352 96.33 %-
all-59410 --
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.281 Å2 / ksol: 0.479 e/Å3
Displacement parametersBiso max: 83.82 Å2 / Biso mean: 17.8294 Å2 / Biso min: 5.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.5284 Å20 Å2-0 Å2
2--0.5284 Å2-0 Å2
3----1.0567 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 36 195 1986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092128
X-RAY DIFFRACTIONf_angle_d1.3162921
X-RAY DIFFRACTIONf_chiral_restr0.074352
X-RAY DIFFRACTIONf_plane_restr0.006375
X-RAY DIFFRACTIONf_dihedral_angle_d16.363781
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.42420.22471330.19872526265991
1.4242-1.45010.21911380.18542566270492
1.4501-1.4780.16841420.16622575271792
1.478-1.50810.15991420.15442603274594
1.5081-1.54090.16981420.14352623276595
1.5409-1.57670.14281320.13982670280295
1.5767-1.61610.16491400.13512672281296
1.6161-1.65980.1381480.13022673282196
1.6598-1.70860.14071350.12362720285597
1.7086-1.76370.13331570.12772679283697
1.7637-1.82670.14091330.12942741287497
1.8267-1.89980.15231380.12792763290198
1.8998-1.98620.12041380.12432777291598
1.9862-2.09080.16991310.12682801293299
2.0908-2.22170.17071310.12462808293999
2.2217-2.39290.14081590.12462787294698
2.3929-2.63320.14631450.13412828297399
2.6332-3.01310.14161340.14292875300999
3.0131-3.79190.15321520.14172905305799
3.7919-19.81370.17031630.16232927309095
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)
10.288-0.1904-0.02260.38730.02380.2486-0.0055-0.067-0.10880.00060.04370.15020.032-0.09350.03610.1085-0.02020.00630.11850.02840.154233.99467.032857.6826
20.10.00430.01370.0240.03540.1045-0.0528-0.0704-0.0959-0.12030.0012-0.03480.1417-0.02640.0010.0853-0.01150.01970.0640.03690.088738.57524.339157.4514
30.2334-0.0380.21330.6143-0.09550.17730.0228-0.0007-0.0449-0.03580.01650.0068-0.02460.01160.04120.0852-0.00410.00580.0860.00060.087246.241712.317752.0035
40.3006-0.07220.03210.0405-0.02160.02580.01590.00650.0387-0.0088-0.0321-0.04430.001-0.0246-00.0987-0.00510.00490.0871-0.0080.101555.357817.884350.3032
50.3002-0.0470.01550.1551-0.06040.1295-0.01710.0374-0.0477-0.02350.07590.04150.04850.04510.02110.11660.00340.00260.0774-0.00040.110257.21977.729753.2373
60.1711-0.03730.0040.1341-0.23240.3380.0610.0869-0.0117-0.0928-0.0727-0.06810.084-0.01370.01080.1060.00860.0020.0907-0.01560.089250.896416.992540.7431
70.2138-0.01030.11690.09080.01190.06990.02620.1475-0.0291-0.0132-0.06650.0055-0.0376-0.0404-0.03310.10030.02050.00170.1025-0.00210.080856.080719.602939.4526
80.47270.3453-0.0820.5566-0.22460.1459-0.05390.0941-0.0535-0.10160.08290.0877-0.02670.05910.00830.1152-0.0099-0.01180.1017-0.0090.085148.913812.58646.1684
90.4317-0.0155-0.00490.24820.00210.06980.00930.2588-0.3279-0.2612-0.11630.1905-0.04060.0441-0.01430.0952-0.01290.00760.0495-0.00080.11643.1106-0.298547.471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:52)A2 - 52
2X-RAY DIFFRACTION2chain 'A' and (resseq 53:65)A53 - 65
3X-RAY DIFFRACTION3chain 'A' and (resseq 66:102)A66 - 102
4X-RAY DIFFRACTION4chain 'A' and (resseq 103:119)A103 - 119
5X-RAY DIFFRACTION5chain 'A' and (resseq 120:144)A120 - 144
6X-RAY DIFFRACTION6chain 'A' and (resseq 145:164)A145 - 164
7X-RAY DIFFRACTION7chain 'A' and (resseq 165:181)A165 - 181
8X-RAY DIFFRACTION8chain 'A' and (resseq 182:214)A182 - 214
9X-RAY DIFFRACTION9chain 'A' and (resseq 215:234)A215 - 234

+
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