[English] 日本語
Yorodumi
- PDB-3ooh: Crystal structure of E. Coli purine nucleoside phosphorylase with PO4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ooh
TitleCrystal structure of E. Coli purine nucleoside phosphorylase with PO4
ComponentsPurine nucleoside phosphorylase deoD-type
KeywordsTRANSFERASE / Purine nucleoside phosphorylase / phosphorylase
Function / homology
Function and homology information


purine nucleoside interconversion / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / DNA damage response / identical protein binding / membrane / cytosol
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
PHOSPHATE ION / : / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsMikleusevic, G. / Stefanic, Z. / Narzyk, M. / Wielgus-Kutrowska, B. / Bzowska, A. / Luic, M.
CitationJournal: Biochimie / Year: 2011
Title: Validation of the catalytic mechanism of Escherichia coli purine nucleoside phosphorylase by structural and kinetic studies.
Authors: Mikleusevic, G. / Stefanic, Z. / Narczyk, M. / Wielgus-Kutrowska, B. / Bzowska, A. / Luic, M.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 14, 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_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: Purine nucleoside phosphorylase deoD-type
B: Purine nucleoside phosphorylase deoD-type
C: Purine nucleoside phosphorylase deoD-type
D: Purine nucleoside phosphorylase deoD-type
E: Purine nucleoside phosphorylase deoD-type
F: Purine nucleoside phosphorylase deoD-type
G: Purine nucleoside phosphorylase deoD-type
H: Purine nucleoside phosphorylase deoD-type
I: Purine nucleoside phosphorylase deoD-type
J: Purine nucleoside phosphorylase deoD-type
K: Purine nucleoside phosphorylase deoD-type
L: Purine nucleoside phosphorylase deoD-type
M: Purine nucleoside phosphorylase deoD-type
N: Purine nucleoside phosphorylase deoD-type
O: Purine nucleoside phosphorylase deoD-type
P: Purine nucleoside phosphorylase deoD-type
Q: Purine nucleoside phosphorylase deoD-type
R: Purine nucleoside phosphorylase deoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)465,17441
Polymers462,98918
Non-polymers2,18423
Water20,7711153
1
A: Purine nucleoside phosphorylase deoD-type
B: Purine nucleoside phosphorylase deoD-type
C: Purine nucleoside phosphorylase deoD-type
D: Purine nucleoside phosphorylase deoD-type
E: Purine nucleoside phosphorylase deoD-type
F: Purine nucleoside phosphorylase deoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,99513
Polymers154,3306
Non-polymers6657
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20950 Å2
ΔGint-135 kcal/mol
Surface area44680 Å2
MethodPISA
2
G: Purine nucleoside phosphorylase deoD-type
H: Purine nucleoside phosphorylase deoD-type
I: Purine nucleoside phosphorylase deoD-type
J: Purine nucleoside phosphorylase deoD-type
K: Purine nucleoside phosphorylase deoD-type
L: Purine nucleoside phosphorylase deoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,18515
Polymers154,3306
Non-polymers8559
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21030 Å2
ΔGint-132 kcal/mol
Surface area44810 Å2
MethodPISA
3
M: Purine nucleoside phosphorylase deoD-type
N: Purine nucleoside phosphorylase deoD-type
O: Purine nucleoside phosphorylase deoD-type
P: Purine nucleoside phosphorylase deoD-type
Q: Purine nucleoside phosphorylase deoD-type
R: Purine nucleoside phosphorylase deoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,99513
Polymers154,3306
Non-polymers6657
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20970 Å2
ΔGint-132 kcal/mol
Surface area44760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.447, 165.923, 135.376
Angle α, β, γ (deg.)90.000, 99.690, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 25721.633 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: deoD, EcDH1_3614 / Plasmid: pSE380 / Production host: Escherichia coli (E. coli) / Strain (production host): HS533
References: UniProt: C9QST6, UniProt: P0ABP8*PLUS, purine-nucleoside phosphorylase
#2: Chemical...
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1153 / 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: 2.3 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 55-75% ammonium phosphate, 50mM citric buffer, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 11, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionRedundancy: 3.32 % / Number: 262054 / Rmerge(I) obs: 0.137 / D res high: 2.9 Å / D res low: 55.72 Å
ReflectionResolution: 2.9→48.2 Å / Num. obs: 89913 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Rmerge(I) allMean I/σ(I) allNum. measured allNum. unique allDiffraction-ID% possible all
2.9-3.060.372.05242507202154.55
3.06-3.240.292.63309509096172.95
3.24-3.470.233.393546910622190.75
3.47-3.740.174.423540510787198.44
3.74-4.10.126.3325239913198.25
4.1-4.590.098.48293738907198.13
4.59-5.290.089.66259707864197.82
5.29-6.480.17.69219366611197.62
6.48-9.170.0612.17169905110197.06
9.17-55.720.0315.791882763195.13

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 39.2
Highest resolutionLowest resolution
Rotation2.53 Å48.16 Å
Translation2.53 Å48.16 Å

-
Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.9 2008/10/21data scaling
DNAdata collection
XDSdata reduction
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K9S

1k9s


Resolution: 2.9→48.163 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.875 / SU ML: 2.91 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1999 2.22 %RANDOM
Rwork0.164 ---
all0.165 ---
obs0.165 78875 98.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 11.332 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso max: 105.1 Å2 / Biso mean: 21.752 Å2 / Biso min: 4.56 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20 Å2-2.333 Å2
2--0.397 Å20 Å2
3----2.376 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32311 0 115 1153 33579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00332925
X-RAY DIFFRACTIONf_angle_d0.63944399
X-RAY DIFFRACTIONf_chiral_restr0.0455058
X-RAY DIFFRACTIONf_plane_restr0.0025740
X-RAY DIFFRACTIONf_dihedral_angle_d14.17711865
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-3.0040.2641990.2188727892699
3.004-3.1240.2641980.2098746894499
3.124-3.2660.2462000.1918744894499
3.266-3.4380.2241990.178752895199
3.438-3.6540.2151990.1618807900699
3.654-3.9350.1842000.1418799899999
3.935-4.3310.1722010.1288817901899
4.331-4.9570.1612000.1238797899799
4.957-6.2440.2142010.168846904799
6.244-48.170.2012020.1818879908198

+
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