[English] 日本語
Yorodumi
- PDB-4lq6: Crystal structure of Rv3717 reveals a novel amidase from M. tuber... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lq6
TitleCrystal structure of Rv3717 reveals a novel amidase from M. tuberculosis
ComponentsN-acetymuramyl-L-alanine amidase-related protein
KeywordsHYDROLASE / Amidase / cell wall hydrolase
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / metal ion binding
Similarity search - Function
Zn-dependent exopeptidases / Ami_3 / N-acetylmuramoyl-L-alanine amidase, catalytic domain / N-acetylmuramoyl-L-alanine amidase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / N-acetymuramyl-L-alanine amidase-related protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.68 Å
AuthorsKumar, A. / Kumar, S. / Kumar, D. / Mishra, A. / Dewangan, R.P. / Shrivastava, P. / Ramachandran, S. / Taneja, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The structure of Rv3717 reveals a novel amidase from Mycobacterium tuberculosis.
Authors: Kumar, A. / Kumar, S. / Kumar, D. / Mishra, A. / Dewangan, R.P. / Shrivastava, P. / Ramachandran, S. / Taneja, B.
History
DepositionJul 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-acetymuramyl-L-alanine amidase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,58510
Polymers22,6961
Non-polymers8899
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.350, 103.780, 129.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-582-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein N-acetymuramyl-L-alanine amidase-related protein


Mass: 22696.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT3820, Rv3717 / Production host: Escherichia coli (E. coli) / References: UniProt: O69684

-
Non-polymers , 5 types, 200 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pt
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.0714 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 16, 2012
RadiationMonochromator: silicon mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0714 Å / Relative weight: 1
ReflectionResolution: 1.68→29.52 Å / Num. all: 29381 / Num. obs: 29381 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.46 Å2
Reflection shellResolution: 1.68→1.74 Å / % possible all: 3.23

-
Processing

Software
NameVersionClassification
HKL-2000data collection
Auto-Rickshawphasing
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.68→21.09 Å / Cor.coef. Fo:Fc: 0.9601 / Cor.coef. Fo:Fc free: 0.9501 / SU R Cruickshank DPI: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1842 1495 5.09 %RANDOM
Rwork0.1605 ---
obs0.1617 29370 99.99 %-
all-29381 --
Displacement parametersBiso mean: 23.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.0235 Å20 Å20 Å2
2---0.237 Å20 Å2
3---0.2605 Å2
Refine analyzeLuzzati coordinate error obs: 0.177 Å
Refinement stepCycle: LAST / Resolution: 1.68→21.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 0 13 191 1760
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011661HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.032265HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d576SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes45HARMONIC2
X-RAY DIFFRACTIONt_gen_planes260HARMONIC5
X-RAY DIFFRACTIONt_it1661HARMONIC20
X-RAY DIFFRACTIONt_nbd13SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion16.32
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion209SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2243SEMIHARMONIC4
LS refinement shellResolution: 1.68→1.74 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.1927 140 4.91 %
Rwork0.1696 2713 -
all0.1709 2853 -
obs--99.99 %
Refinement TLS params.Method: refined / Origin x: 10.6726 Å / Origin y: 40.9984 Å / Origin z: 45.2963 Å
111213212223313233
T-0.0491 Å2-0.0049 Å2-0.0364 Å2--0.0435 Å20.026 Å2---0.0244 Å2
L1.2034 °20.061 °2-0.0197 °2-1.1342 °20.1276 °2--0.9346 °2
S-0.0372 Å °0.079 Å °0.1692 Å °0.0299 Å °0.0349 Å °-0.0491 Å °-0.0604 Å °0.0387 Å °0.0023 Å °
Refinement TLS groupSelection details: { A|2 - 214 }

+
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