[English] 日本語
Yorodumi
- PDB-4xt4: Crystal structure of Rv2671 from Mycobacteirum tuberculosis in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xt4
TitleCrystal structure of Rv2671 from Mycobacteirum tuberculosis in complex with dihydropteridine ring of dihydropteroic acid
ComponentsRv2671
KeywordsOXIDOREDUCTASE / reductase / pteridine / Structural Genomics / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


5-amino-6-(5-phosphoribosylamino)uracil reductase activity / riboflavin biosynthetic process / nucleotide binding / cytosol
Similarity search - Function
: / Bacterial bifunctional deaminase-reductase, C-terminal / RibD C-terminal domain / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-amino-6-methyl-7,8-dihydropteridin-4(3H)-one / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Bacterial bifunctional deaminase-reductase C-terminal domain-containing protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.891 Å
AuthorsSacchettini, J.C. / Cheng, Y.S. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI107774 United States
R. J. Wolfe-Welch FoundationA-0015 United States
CitationJournal: Biochemistry / Year: 2016
Title: Structural Insights into Mycobacterium tuberculosis Rv2671 Protein as a Dihydrofolate Reductase Functional Analogue Contributing to para-Aminosalicylic Acid Resistance.
Authors: Cheng, Y.S. / Sacchettini, J.C.
History
DepositionJan 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rv2671
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8285
Polymers27,7211
Non-polymers1,1074
Water1,47782
1
A: Rv2671
hetero molecules

A: Rv2671
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,65710
Polymers55,4432
Non-polymers2,2148
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area8460 Å2
ΔGint-36 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.281, 94.427, 75.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-442-

HOH

-
Components

#1: Protein Rv2671


Mass: 27721.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: ribD, Rv2671, RVBD_2671, LH57_14640, P425_02787 / Production host: Escherichia coli (E. coli) / References: UniProt: P71968
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-44W / 2-amino-6-methyl-7,8-dihydropteridin-4(3H)-one


Mass: 179.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M sodium chloride, 25% PEG 3350, 0.1M Bis-Tris pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 20431 / % possible obs: 99.5 % / Redundancy: 9.3 % / Biso Wilson estimate: 28.61 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.024 / Rrim(I) all: 0.074 / Χ2: 0.945 / Net I/av σ(I): 36.842 / Net I/σ(I): 8.6 / Num. measured all: 189305
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.89-1.926.60.5859360.9230.2330.6310.56193.4
1.92-1.967.50.5769960.910.2170.6170.57496.5
1.96-28.30.4619810.9610.1650.490.62199.6
2-2.048.90.4310060.9590.1490.4560.61100
2.04-2.089.20.35210170.9790.1210.3720.628100
2.08-2.139.40.28610080.9860.0970.3030.639100
2.13-2.189.60.25210290.9860.0850.2670.659100
2.18-2.249.70.22710030.990.0760.240.717100
2.24-2.319.80.19610140.9920.0660.2070.711100
2.31-2.389.80.16910210.9940.0570.1790.75100
2.38-2.479.80.14410330.9960.0480.1520.798100
2.47-2.579.80.12310130.9960.0410.130.844100
2.57-2.689.80.10710210.9970.0360.1130.862100
2.68-2.829.80.08610400.9980.0290.0910.914100
2.82-39.80.07110160.9980.0240.0750.987100
3-3.239.70.05910320.9980.020.0631.152100
3.23-3.569.70.05810420.9980.0190.0611.653100
3.56-4.079.50.05710370.9980.0190.062.149100
4.07-5.139.30.04210650.9990.0150.0451.735100
5.13-508.90.0311210.9990.0110.0320.96599.6

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
SBC-Collectdata collection
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2p4g

2p4g


Resolution: 1.891→35.14 Å / FOM work R set: 0.8232 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 1043 5.11 %
Rwork0.1877 19359 -
obs0.1895 20402 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.42 Å2 / Biso mean: 33.37 Å2 / Biso min: 14.81 Å2
Refinement stepCycle: final / Resolution: 1.891→35.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 56 82 2002
Biso mean--36.21 36.21 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081948
X-RAY DIFFRACTIONf_angle_d1.2412653
X-RAY DIFFRACTIONf_chiral_restr0.08311
X-RAY DIFFRACTIONf_plane_restr0.005339
X-RAY DIFFRACTIONf_dihedral_angle_d18.945721
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8906-1.99030.32811530.24352597275096
1.9903-2.11490.24261510.197427452896100
2.1149-2.27820.2471480.191227412889100
2.2782-2.50740.23351520.185627732925100
2.5074-2.87010.20421440.189227752919100
2.8701-3.61540.2441540.184228002954100
3.6154-35.14660.19081410.181229283069100

+
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