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- PDB-4xt7: Crystal structure of Rv2671 from Mycobacterium tuberculosis in co... -

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Basic information

Entry
Database: PDB / ID: 4xt7
TitleCrystal structure of Rv2671 from Mycobacterium tuberculosis in complex with NADP+ and trimethoprim
ComponentsRv2671
KeywordsOXIDOREDUCTASE / trimethoprim / reductase / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / TRIMETHOPRIM / Bacterial bifunctional deaminase-reductase C-terminal domain-containing protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 Foundation 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)28,9535
Polymers27,7211
Non-polymers1,2324
Water1,18966
1
A: Rv2671
hetero molecules

A: Rv2671
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,90710
Polymers55,4432
Non-polymers2,4648
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area10490 Å2
ΔGint-42 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.017, 93.128, 74.572
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-427-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 70 molecules

#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-TOP / TRIMETHOPRIM


Mass: 290.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18N4O3 / Comment: antibiotic*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M sodium chloride, 25% PEG3350, 0.1M Bis-Tris pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98011 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 11070 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 25.65 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.034 / Rrim(I) all: 0.092 / Χ2: 1.352 / Net I/av σ(I): 28.571 / Net I/σ(I): 9.2 / Num. measured all: 81136
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2
2.3-2.347.40.3535520.9570.1390.3791.061
2.34-2.387.50.3185390.9610.1240.3421.165
2.38-2.437.40.2835510.9740.1110.3041.147
2.43-2.487.40.2625310.9730.1030.2821.114
2.48-2.537.50.245440.9790.0930.2571.115
2.53-2.597.40.2285380.9830.0890.2451.1
2.59-2.667.50.2025680.980.0790.2171.216
2.66-2.737.40.1865210.9880.0730.21.248
2.73-2.817.40.1645510.9880.0640.1761.303
2.81-2.97.40.1455610.9910.0570.1561.321
2.9-37.40.1265380.9930.0490.1361.426
3-3.127.40.1055420.9950.0410.1131.487
3.12-3.267.40.095620.9960.0350.0961.39
3.26-3.447.40.0755490.9960.030.0811.301
3.44-3.657.40.0625620.9970.0240.0671.345
3.65-3.937.30.0625520.9970.0250.0671.713
3.93-4.337.20.0575540.9980.0230.0622.188
4.33-4.957.20.0445690.9980.0180.0481.674
4.95-6.247.20.0465720.9980.0190.051.298
6.24-506.60.046140.9970.0170.0431.446

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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: 2.3→46.564 Å / FOM work R set: 0.8213 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2221 529 4.79 %
Rwork0.1745 10526 -
obs0.1768 11055 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.68 Å2 / Biso mean: 29.08 Å2 / Biso min: 11.53 Å2
Refinement stepCycle: final / Resolution: 2.3→46.564 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 82 66 2006
Biso mean--31.1 28.98 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011970
X-RAY DIFFRACTIONf_angle_d1.3642684
X-RAY DIFFRACTIONf_chiral_restr0.074315
X-RAY DIFFRACTIONf_plane_restr0.005340
X-RAY DIFFRACTIONf_dihedral_angle_d21.26729
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2962-2.52730.28151210.186225922713
2.5273-2.89290.27011390.19325972736
2.8929-3.64460.19491390.165826122751
3.6446-46.57360.20181300.169327252855

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