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- PDB-4xt4: Crystal structure of Rv2671 from Mycobacteirum tuberculosis in co... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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 / Nicotinamide adenine dinucleotide phosphate


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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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: 0

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

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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

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