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- PDB-4xt8: Crystal structure of Rv2671 from Mycobacterium tuberculosis in co... -

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Basic information

Entry
Database: PDB / ID: 4xt8
TitleCrystal structure of Rv2671 from Mycobacterium tuberculosis in complex with NADP+ and trimetrexate
ComponentsRv2671
KeywordsOXIDOREDUCTASE / trimetrexate / 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 / TRIMETREXATE / Bacterial bifunctional deaminase-reductase C-terminal domain-containing protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)29,2648
Polymers27,7211
Non-polymers1,5427
Water1,51384
1
A: Rv2671
hetero molecules

A: Rv2671
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,52816
Polymers55,4432
Non-polymers3,08514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area12430 Å2
ΔGint-3 kcal/mol
Surface area17790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.391, 93.612, 74.320
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-419-

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 , 6 types, 91 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-TMQ / TRIMETREXATE


Mass: 370.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24N5O3 / Comment: inhibitor*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M sodium chloride, 25% PEG3350, 0.1M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98011 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / 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: 1.95→50 Å / Num. obs: 18001 / % possible obs: 99.9 % / Redundancy: 8.6 % / Biso Wilson estimate: 25.95 Å2 / Rmerge(I) obs: 0.08 / Χ2: 2.972 / Net I/av σ(I): 54.129 / Net I/σ(I): 15.3 / Num. measured all: 155567
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.95-1.988.80.2888692.083100
1.98-2.028.90.2698951.999100
2.02-2.0690.2398862.298100
2.06-2.18.90.2128992.295100
2.1-2.158.90.1988782.534100
2.15-2.28.90.189032.56100
2.2-2.258.80.178812.604100
2.25-2.318.90.1628922.686100
2.31-2.388.80.1448772.8599.9
2.38-2.468.70.1258872.821100
2.46-2.548.70.1249073.01100
2.54-2.658.50.1158873.336100
2.65-2.778.60.1059103.418100
2.77-2.918.60.0938963.55499.9
2.91-3.18.50.0828953.54100
3.1-3.338.40.0779003.82999.9
3.33-3.678.20.0729164.06699.9
3.67-4.28.20.0649114.08499.8
4.2-5.298.50.0599363.70999.9
5.29-508.30.0479762.40899.3

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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: 1.95→46.806 Å / FOM work R set: 0.839 / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 919 5.11 %
Rwork0.1782 17053 -
obs0.1804 17972 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.46 Å2 / Biso mean: 26.51 Å2 / Biso min: 10.9 Å2
Refinement stepCycle: final / Resolution: 1.95→46.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 103 84 2045
Biso mean--28.07 31.22 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092020
X-RAY DIFFRACTIONf_angle_d1.2992753
X-RAY DIFFRACTIONf_chiral_restr0.07320
X-RAY DIFFRACTIONf_plane_restr0.005349
X-RAY DIFFRACTIONf_dihedral_angle_d20.693746
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9501-2.05290.26111260.180423922518
2.0529-2.18150.22431350.176523962531
2.1815-2.34990.27181100.180924382548
2.3499-2.58640.2531340.184323942528
2.5864-2.96060.24371410.189824372578
2.9606-3.72980.21551420.173524412583
3.7298-46.81950.19141310.174425552686

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