[English] 日本語
Yorodumi
- PDB-3uao: Structure and Catalytic Mechanism of the Vitamin B3 Degradative E... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uao
TitleStructure and Catalytic Mechanism of the Vitamin B3 Degradative Enzyme Maleamate Amidohydrolase from Bordetalla bronchiseptica RB50
ComponentsPutative isochorismatase
KeywordsHYDROLASE / Rossmann fold / maleamate
Function / homology
Function and homology information


Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Isochorismatase / Putative isochorismatase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.399 Å
AuthorsKincaid, V.A. / Sullivan, E.D. / Klein, R.D. / Rowlett, R.S. / Snider, M.J.
CitationJournal: Biochemistry / Year: 2012
Title: Structure and Catalytic Mechanism of Nicotinate (Vitamin B(3)) Degradative Enzyme Maleamate Amidohydrolase from Bordetella bronchiseptica RB50.
Authors: Kincaid, V.A. / Sullivan, E.D. / Klein, R.D. / Noel, J.W. / Rowlett, R.S. / Snider, M.J.
History
DepositionOct 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Database references
Revision 1.2Sep 13, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative isochorismatase
B: Putative isochorismatase
C: Putative isochorismatase
D: Putative isochorismatase
E: Putative isochorismatase
F: Putative isochorismatase
G: Putative isochorismatase
H: Putative isochorismatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,11724
Polymers202,1728
Non-polymers94516
Water10,377576
1
A: Putative isochorismatase
B: Putative isochorismatase
F: Putative isochorismatase
H: Putative isochorismatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,55812
Polymers101,0864
Non-polymers4728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13720 Å2
ΔGint-56 kcal/mol
Surface area23800 Å2
MethodPISA
2
C: Putative isochorismatase
D: Putative isochorismatase
E: Putative isochorismatase
G: Putative isochorismatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,55812
Polymers101,0864
Non-polymers4728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13600 Å2
ΔGint-51 kcal/mol
Surface area23820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.560, 157.560, 198.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein
Putative isochorismatase /


Mass: 25271.492 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: RB5 / Gene: BB0275, BB1782 / Plasmid: pTHT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7TTE5, UniProt: A0A0H3LKK8*PLUS, EC: 3.5.1.107
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammonium acetate, 0.1 M sodium cacodylate, 30% PEG-8000, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD RUBY CCD / Detector: CCD / Date: Aug 31, 2010 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.611
11-H-K, K, -L20.389
ReflectionResolution: 2.399→12.01 Å / Num. all: 143682 / Num. obs: 131825 / % possible obs: 91.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.2 % / Rsym value: 0.087 / Net I/σ(I): 9.78
Reflection shellResolution: 2.399→2.52 Å / Redundancy: 1.2 % / Num. unique all: 13186 / Rsym value: 0.271 / % possible all: 67.5

-
Processing

Software
NameVersionClassification
CrysalisProdata collection
PHASERphasing
REFMAC5.5.0109refinement
CrysalisProdata reduction
CrysalisProdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NBA MODIFIED TO TARGET SEQUENCE USING PHYRE SERVER

1nba


Resolution: 2.399→12.01 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.164 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17252 1368 2 %RANDOM
Rwork0.12704 ---
obs0.12796 131825 97.94 %-
all-143682 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.739 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---0.63 Å20 Å2
3---1.25 Å2
Refinement stepCycle: LAST / Resolution: 2.399→12.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11822 0 64 576 12462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02212118
X-RAY DIFFRACTIONr_bond_other_d0.0010.027964
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.95816463
X-RAY DIFFRACTIONr_angle_other_deg1.133319357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0775.11605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65623.015481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.308151800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4571588
X-RAY DIFFRACTIONr_chiral_restr0.0970.21867
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022517
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_it0.6511.57953
X-RAY DIFFRACTIONr_mcbond_other0.1371.53255
X-RAY DIFFRACTIONr_mcangle_it1.136212573
X-RAY DIFFRACTIONr_scbond_it1.89134165
X-RAY DIFFRACTIONr_scangle_it3.0474.53890
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.399→2.459 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 78 -
Rwork0.172 3733 -
obs--74.46 %
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)
10.54450.10110.30020.75570.4420.5111-0.0017-0.0175-0.0343-0.2321-0.120.0801-0.117-0.00130.12170.18960.0488-0.0440.0748-0.00720.047433.1443.7318.161
20.5188-0.03170.04250.61190.21130.3194-0.0225-0.00560.00970.1273-0.04090.10240.0138-0.03030.06350.1385-0.02370.03750.0936-0.01070.066529.77947.03741.84
30.9598-0.26370.06880.15420.02330.4174-0.0148-0.1615-0.1098-0.01610.02170.0107-0.02410.0568-0.00690.05260.00520.00270.13720.05790.099454.377-2.76870.419
40.8097-0.12830.06290.43970.18410.4930.0126-0.0478-0.0127-0.00780.00690.0802-0.0156-0.0551-0.01960.0612-0.004-0.00110.08710.02020.110125.21411.52360.359
50.8285-0.1158-0.13160.49030.18790.63040.01320.0387-0.0545-0.0077-0.0303-0.0575-0.02660.02680.01710.0607-0.001-0.00210.08620.01560.089954.4355.26147.61
60.52990.03880.15180.77490.28830.30060.0035-0.0149-0.0018-0.0229-0.00220.0296-0.09490.0436-0.00130.1305-0.01570.00830.08180.00030.050346.10861.65432.007
70.90050.34750.1190.17520.15750.5487-0.01460.0101-0.2684-0.00710.0240.0162-0.0846-0.0379-0.00940.04150.0112-0.01380.04610.01360.239726.546-12.37456.725
80.58930.0886-0.00220.81670.24050.39110.02560.0346-0.0533-0.0289-0.04780.00820.01720.0450.02220.1110.0148-0.01250.082-0.00020.059647.11629.26521.063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 203
2X-RAY DIFFRACTION1A215 - 252
3X-RAY DIFFRACTION2B5 - 204
4X-RAY DIFFRACTION2B216 - 416
5X-RAY DIFFRACTION3C5 - 205
6X-RAY DIFFRACTION3C215 - 450
7X-RAY DIFFRACTION4D6 - 205
8X-RAY DIFFRACTION4D215 - 423
9X-RAY DIFFRACTION5E5 - 205
10X-RAY DIFFRACTION5E216 - 442
11X-RAY DIFFRACTION6F7 - 205
12X-RAY DIFFRACTION6F215 - 448
13X-RAY DIFFRACTION7G7 - 204
14X-RAY DIFFRACTION7G215 - 458
15X-RAY DIFFRACTION8H7 - 204
16X-RAY DIFFRACTION8H216 - 480

+
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