[English] 日本語
Yorodumi
- PDB-3ztv: Structure of Haemophilus influenzae NAD nucleotidase (NadN) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ztv
TitleStructure of Haemophilus influenzae NAD nucleotidase (NadN)
ComponentsNAD NUCLEOTIDASE
KeywordsHYDROLASE / NAD PYROPHOSPHATASE / NMN NUCLEOTIDASE / PERIPLASMIC ENZYME / CD73
Function / homology
Function and homology information


UDP-sugar diphosphatase activity / nucleotide catabolic process / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / outer membrane-bounded periplasmic space / nucleotide binding / metal ion binding
Similarity search - Function
NAD pyrophosphatase/5-nucleotidase NadN / 5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal domain / 5'-nucleotidase signature 1. / 5'-Nucleotidase, conserved site / 5'-nucleotidase signature 2. / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily ...NAD pyrophosphatase/5-nucleotidase NadN / 5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal domain / 5'-nucleotidase signature 1. / 5'-Nucleotidase, conserved site / 5'-nucleotidase signature 2. / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / NAD 5'-nucleotidase / NAD nucleotidase
Similarity search - Component
Biological speciesHAEMOPHILUS INFLUENZAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsGaravaglia, S. / Bruzzone, S. / Cassani, C. / Canella, L. / Allegrone, G. / Sturla, L. / Mannino, E. / Millo, E. / De Flora, A. / Rizzi, M.
CitationJournal: Biochem.J. / Year: 2012
Title: The High-Resolution Crystal Structure of Periplasmic Haemophilus Influenzae Nad Nucleotidase Reveals a Novel Enzymatic Function of Human Cd73 Related to Nad Metabolism.
Authors: Garavaglia, S. / Bruzzone, S. / Cassani, C. / Canella, L. / Allegrone, G. / Sturla, L. / Mannino, E. / Millo, E. / De Flora, A. / Rizzi, M.
History
DepositionJul 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: NAD NUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2535
Polymers63,7631
Non-polymers4904
Water11,331629
1
A: NAD NUCLEOTIDASE
hetero molecules

A: NAD NUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,50610
Polymers127,5262
Non-polymers9808
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area3220 Å2
ΔGint-167.3 kcal/mol
Surface area43390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.640, 126.607, 200.486
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2302-

HOH

-
Components

#1: Protein NAD NUCLEOTIDASE / NADN


Mass: 63763.074 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-603
Source method: isolated from a genetically manipulated source
Details: FRAGMENT CORRESPONDS TO MATURE PROTEIN / Source: (gene. exp.) HAEMOPHILUS INFLUENZAE (bacteria) / Strain: RD KW20 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q4QNY4, UniProt: P44569*PLUS, 5'-nucleotidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 629 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 26 RESIDUES CORRESPONDING TO THE SIGNAL PEPTIDE (PELB) WERE CLEAVED OFF IN THE ...THE FIRST 26 RESIDUES CORRESPONDING TO THE SIGNAL PEPTIDE (PELB) WERE CLEAVED OFF IN THE RECOMBINANT ENZYME CRYSTALLIZED.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 6.5 / Details: 25% P/V PEG 1500, 0.1 M MES, PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. obs: 166343 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 8.86 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.1
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.1 / % possible all: 94

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z1A

2z1a


Resolution: 1.3→31.687 Å / SU ML: 0.16 / σ(F): 1.13 / Phase error: 22.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2342 1479 0.5 %
Rwork0.2003 --
obs0.2005 162525 94.9 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.813 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.8311 Å20 Å20 Å2
2--3.9137 Å20 Å2
3----2.0826 Å2
Refinement stepCycle: LAST / Resolution: 1.3→31.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4391 0 27 629 5047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064510
X-RAY DIFFRACTIONf_angle_d1.0666104
X-RAY DIFFRACTIONf_dihedral_angle_d12.0651658
X-RAY DIFFRACTIONf_chiral_restr0.076677
X-RAY DIFFRACTIONf_plane_restr0.005786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.34650.2641540.274628591X-RAY DIFFRACTION87
1.3465-1.40040.24741450.234330036X-RAY DIFFRACTION91
1.4004-1.46410.21541560.218330653X-RAY DIFFRACTION93
1.4641-1.54130.21831020.201631082X-RAY DIFFRACTION94
1.5413-1.63790.20091620.188231384X-RAY DIFFRACTION95
1.6379-1.76430.23421340.189131734X-RAY DIFFRACTION96
1.7643-1.94180.30281480.218831860X-RAY DIFFRACTION97
1.9418-2.22280.22261360.188532404X-RAY DIFFRACTION98
2.2228-2.80020.24061630.202432533X-RAY DIFFRACTION99
2.8002-31.69660.22061790.185231858X-RAY DIFFRACTION97

+
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