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- PDB-4xt6: Crystal structure of Rv2671 from Mycobacterium tuberculosis in co... -

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Basic information

Entry
Database: PDB / ID: 4xt6
TitleCrystal structure of Rv2671 from Mycobacterium tuberculosis in complex with the tetrahydropteridine ring of tetrahydrofolate (THF)
ComponentsRv2671
KeywordsOXIDOREDUCTASE / tetrahydrofolate (THF) / reductase / NADP+ / 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
Chem-44V / 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: 1.85 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 23, 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)28,6463
Polymers27,7211
Non-polymers9252
Water1,36976
1
A: Rv2671
hetero molecules

A: Rv2671
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2926
Polymers55,4432
Non-polymers1,8494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area7290 Å2
ΔGint-37 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.428, 96.016, 76.107
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-426-

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


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-44V / (6S)-2-amino-6-methyl-5,6,7,8-tetrahydropteridin-4(3H)-one


Mass: 181.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11N5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.43 Å3/Da / Density % sol: 49.35 %
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: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 22264 / % possible obs: 99.4 % / Redundancy: 8.7 % / Biso Wilson estimate: 27.05 Å2 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.019 / Rrim(I) all: 0.056 / Χ2: 1.675 / Net I/av σ(I): 55.291 / Net I/σ(I): 15.1 / Num. measured all: 194557
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.8890.27410910.9840.0950.290.939100
1.88-1.9290.2411060.9880.0830.2551.014100
1.92-1.9590.21310980.990.0730.2261.017100
1.95-1.9990.17810940.9920.0610.1881.057100
1.99-2.0490.1511180.9930.0520.1591.134100
2.04-2.088.90.12911050.9950.0450.1361.196100
2.08-2.1490.1111110.9960.0380.1161.265100
2.14-2.1990.09811060.9950.0340.1041.316100
2.19-2.2690.08910970.9970.0310.0941.412100
2.26-2.3390.08611120.9970.030.0911.488100
2.33-2.4190.07711160.9970.0270.0811.48100
2.41-2.518.90.0711060.9980.0240.0741.643100
2.51-2.638.90.06811310.9980.0240.0721.896100
2.63-2.768.90.06611180.9980.0230.072.124100
2.76-2.948.80.06611130.9970.0230.072.54100
2.94-3.168.60.06111320.9980.0220.0652.958100
3.16-3.488.40.05311350.9980.0190.0573.038100
3.48-3.998.10.04111450.9990.0150.0442.48999.9
3.99-5.0280.03511210.9980.0130.0371.9697.9
5.02-507.50.03311090.9980.0130.0351.75190.8

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Processing

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

2p4g


Resolution: 1.85→31.612 Å / FOM work R set: 0.8266 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2421 1135 5.1 %
Rwork0.1968 21105 -
obs0.199 22240 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.81 Å2 / Biso mean: 30.86 Å2 / Biso min: 11.79 Å2
Refinement stepCycle: final / Resolution: 1.85→31.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 44 76 1905
Biso mean--35.78 33.72 -
Num. residues----237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081871
X-RAY DIFFRACTIONf_angle_d1.2292553
X-RAY DIFFRACTIONf_chiral_restr0.078307
X-RAY DIFFRACTIONf_plane_restr0.005323
X-RAY DIFFRACTIONf_dihedral_angle_d18.994685
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.93410.2731570.205525792736100
1.9341-2.03610.27191480.204826152763100
2.0361-2.16360.26421440.195726052749100
2.1636-2.33060.25341300.206926472777100
2.3306-2.56510.25691470.207826422789100
2.5651-2.9360.2781390.209326562795100
2.936-3.69820.2371450.196326882833100
3.6982-31.6170.20761250.18472673279895

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