[English] 日本語
Yorodumi
- PDB-4l08: Crystal structure of the maleamate amidase Ami(C149A) in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4l08
TitleCrystal structure of the maleamate amidase Ami(C149A) in complex with maleate from Pseudomonas putida S16
ComponentsHydrolase, isochorismatase family
KeywordsHYDROLASE / maleamate amidase
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
MALEIC ACID / Maleamate amidase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsChen, D.D. / Lu, Y. / Zhang, Z. / Wu, G. / Xu, P.
CitationJournal: Mol.Microbiol. / Year: 2014
Title: Structural insights into the specific recognition of N-heterocycle biodenitrogenation-derived substrates by microbial amide hydrolases.
Authors: Wu, G. / Chen, D. / Tang, H. / Ren, Y. / Chen, Q. / Lv, Y. / Zhang, Z. / Zhao, Y.L. / Yao, Y. / Xu, P.
History
DepositionMay 31, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Structure summary
Revision 1.2Dec 28, 2016Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: Hydrolase, isochorismatase family
A: Hydrolase, isochorismatase family
C: Hydrolase, isochorismatase family
D: Hydrolase, isochorismatase family
E: Hydrolase, isochorismatase family
F: Hydrolase, isochorismatase family
G: Hydrolase, isochorismatase family
H: Hydrolase, isochorismatase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,01716
Polymers177,0888
Non-polymers9298
Water905
1
B: Hydrolase, isochorismatase family
E: Hydrolase, isochorismatase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5044
Polymers44,2722
Non-polymers2322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-6 kcal/mol
Surface area15240 Å2
MethodPISA
2
A: Hydrolase, isochorismatase family
G: Hydrolase, isochorismatase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5044
Polymers44,2722
Non-polymers2322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-6 kcal/mol
Surface area15260 Å2
MethodPISA
3
C: Hydrolase, isochorismatase family
F: Hydrolase, isochorismatase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5044
Polymers44,2722
Non-polymers2322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-7 kcal/mol
Surface area15390 Å2
MethodPISA
4
D: Hydrolase, isochorismatase family
H: Hydrolase, isochorismatase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5044
Polymers44,2722
Non-polymers2322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-6 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.449, 167.045, 175.018
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein
Hydrolase, isochorismatase family / Maleamate amidase


Mass: 22136.059 Da / Num. of mol.: 8 / Mutation: C149A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: S16 / Gene: PPS_4057 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F8G0M0
#2: Chemical
ChemComp-MAE / MALEIC ACID


Mass: 116.072 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.07 Å3/Da / Density % sol: 59.97 % / Mosaicity: 0.934 °
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.1M sodium citrate, pH 5.8, 19% polyethylene glycol monomethylether 5000, vapor diffusion, hanging drop, temperature 287K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Wavelength: 1 Å
DetectorDetector: CCD / Date: Feb 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→120.84 Å / Num. obs: 63356 / % possible obs: 99.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.093 / Χ2: 1.011 / Net I/σ(I): 19.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.65-2.746.60.33962561.0571100
2.74-2.856.60.2762831.0221100
2.85-2.986.70.21362480.9691100
2.98-3.146.80.15862891.0291100
3.14-3.3470.133629411100
3.34-3.670.12163191.0611100
3.6-3.9670.11363461.021199.9
3.96-4.5370.08663390.993199.9
4.53-5.716.90.06664720.99199.9
5.71-506.80.05965100.969197.2

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 12.622 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.657 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2545 3195 5.1 %RANDOM
Rwork0.2221 ---
obs0.2237 62880 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.95 Å2 / Biso mean: 60.0688 Å2 / Biso min: 35.52 Å2
Baniso -1Baniso -2Baniso -3
1-6.08 Å20 Å20 Å2
2---2.09 Å20 Å2
3----3.99 Å2
Refinement stepCycle: LAST / Resolution: 2.66→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12255 0 64 5 12324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212559
X-RAY DIFFRACTIONr_angle_refined_deg1.0241.96517109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4751640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32324.213470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.61151931
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6541556
X-RAY DIFFRACTIONr_chiral_restr0.0710.22016
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219472
LS refinement shellResolution: 2.658→2.727 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 222 -
Rwork0.415 3851 -
all-4073 -
obs--93.68 %

+
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