[English] 日本語
Yorodumi
- PDB-29iv: Crystal structure of Borrelia burgdorferi nicotinamidase BBE22 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 29iv
TitleCrystal structure of Borrelia burgdorferi nicotinamidase BBE22
Componentsnicotinamidase
KeywordsCYTOSOLIC PROTEIN / Lyme disease / borreliosis / PncA / nicotinamidase
Function / homology
Function and homology information


pyridine nucleotide biosynthetic process / nicotinamidase / nicotinamidase activity / metal ion binding
Similarity search - Function
: / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain
Similarity search - Domain/homology
NICOTINIC ACID / nicotinamidase
Similarity search - Component
Biological speciesBorreliella burgdorferi B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBrangulis, K.
Funding support Latvia, 1items
OrganizationGrant numberCountry
Other government.5.2.1.1.i.0/2/24/I/CFLA/001 Latvia
CitationJournal: Febs Open Bio / Year: 2026
Title: The crystal structure of the Borrelia burgdorferi nicotinamidase BBE22 resolves a long-standing annotation error.
Authors: Brangulis, K.
History
DepositionMar 15, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: nicotinamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0663
Polymers22,8771
Non-polymers1892
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-35 kcal/mol
Surface area8880 Å2
Unit cell
Length a, b, c (Å)36.343, 45.210, 115.212
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein nicotinamidase / Nicotinamide deamidase


Mass: 22877.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first 4 residues (GAMG) are remnants from the expression tag.
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: pncA / Plasmid: pETm-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G1FKW2, nicotinamidase
#2: Chemical ChemComp-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Bis-Tris pH 5.5 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 10, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 3.2→115.21 Å / Num. obs: 3391 / % possible obs: 97.8 % / Redundancy: 12.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.191 / Net I/σ(I): 10.2
Reflection shellResolution: 3.2→3.42 Å / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 5.4 / Num. unique obs: 603 / CC1/2: 0.97

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→42.12 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.89 / SU B: 27.378 / SU ML: 0.47 / Cross valid method: THROUGHOUT / ESU R Free: 0.602 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26287 162 4.8 %RANDOM
Rwork0.20445 ---
obs0.20737 3197 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.794 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.08 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 3.2→42.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1549 0 10 0 1559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131589
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161497
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.6312150
X-RAY DIFFRACTIONr_angle_other_deg1.1921.5843449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3285192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.21325.25678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.07715284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.862153
X-RAY DIFFRACTIONr_chiral_restr0.0670.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021802
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02371
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_it1.9323.006771
X-RAY DIFFRACTIONr_mcbond_other1.9283.002770
X-RAY DIFFRACTIONr_mcangle_it3.2444.497962
X-RAY DIFFRACTIONr_mcangle_other3.2424.501963
X-RAY DIFFRACTIONr_scbond_it2.1923.354818
X-RAY DIFFRACTIONr_scbond_other2.1473.345817
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6934.9081188
X-RAY DIFFRACTIONr_long_range_B_refined6.73435.541785
X-RAY DIFFRACTIONr_long_range_B_other6.73235.5511786
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.491 13 -
Rwork0.249 236 -
obs--100 %

+
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