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- PDB-4xrb: Crystal structure of Rv2671 from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 4xrb
TitleCrystal structure of Rv2671 from Mycobacterium tuberculosis
ComponentsRV2671
KeywordsOXIDOREDUCTASE / 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
Chem-NDP / DI(HYDROXYETHYL)ETHER / Bacterial bifunctional deaminase-reductase C-terminal domain-containing protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCheng, Y.S. / Sacchettini, J.C. / 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 20, 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: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)28,5733
Polymers27,7211
Non-polymers8522
Water1,22568
1
A: RV2671
hetero molecules

A: RV2671
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1466
Polymers55,4432
Non-polymers1,7034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area9390 Å2
ΔGint-41 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.355, 96.608, 75.525
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-428-

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 (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-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 68 / 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: 49.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG3350, 0.2M sodium chloride, 0.1M Bis(2-hydroxyethyl)-amino-tris(hydroxymethyl)-methane) pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 21013 / % possible obs: 99.3 % / Redundancy: 7.1 % / Biso Wilson estimate: 29.45 Å2 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.019 / Rrim(I) all: 0.049 / Χ2: 1.439 / Net I/av σ(I): 50.876 / Net I/σ(I): 15.8 / Num. measured all: 149934
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.937.30.2910440.9610.1160.3121.042100
1.93-1.977.30.24210170.9770.0960.2610.959100
1.97-2.017.30.20310570.9840.0810.2180.98100
2.01-2.057.30.16210330.9890.0640.1750.969100
2.05-2.097.30.15410580.9890.0620.1661.059100
2.09-2.147.30.11610190.9940.0460.1250.995100
2.14-2.197.30.110540.9960.0390.1071.034100
2.19-2.257.30.08710480.9960.0340.0931.104100
2.25-2.327.30.08410540.9970.0330.091.129100
2.32-2.397.30.07710410.9970.030.0821.122100
2.39-2.487.30.06810520.9970.0270.0731.221100
2.48-2.587.30.06810510.9960.0270.0741.443100
2.58-2.77.20.06810540.9970.0270.0731.836100
2.7-2.847.20.06410610.9970.0250.0692.036100
2.84-3.027.10.05810680.9970.0230.0622.208100
3.02-3.257.10.04710610.9980.0190.0512.104100
3.25-3.586.90.03710690.9990.0150.042.008100
3.58-4.096.90.03110710.9990.0130.0341.86299.9
4.09-5.166.70.03110660.9980.0130.0331.84697.8
5.16-506.10.03410350.9980.0150.0372.01889.5

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Processing

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

2p4g


Resolution: 1.9→27.358 Å / FOM work R set: 0.86 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2005 1077 5.13 %
Rwork0.1756 19916 -
obs0.1768 20993 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.14 Å2 / Biso mean: 36.43 Å2 / Biso min: 14.48 Å2
Refinement stepCycle: final / Resolution: 1.9→27.358 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1851 0 52 68 1971
Biso mean--48.7 38.93 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181935
X-RAY DIFFRACTIONf_angle_d1.9562640
X-RAY DIFFRACTIONf_chiral_restr0.137316
X-RAY DIFFRACTIONf_plane_restr0.007339
X-RAY DIFFRACTIONf_dihedral_angle_d15.408715
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 (%)
1.8924-1.97860.2481370.20052413255099
1.9786-2.08280.21691410.18524872628100
2.0828-2.21330.2211450.172624672612100
2.2133-2.38410.19641300.176824772607100
2.3841-2.62380.25221260.179225142640100
2.6238-3.00310.21491550.181824962651100
3.0031-3.7820.18071240.168725442668100
3.782-27.36130.17971190.17292518263795
Refinement TLS params.Method: refined / Origin x: 19.8749 Å / Origin y: 27.2598 Å / Origin z: 12.5363 Å
111213212223313233
T0.1724 Å2-0.0119 Å20.009 Å2-0.1755 Å20.0348 Å2--0.1346 Å2
L1.8934 °20.592 °20.4057 °2-1.5735 °20.2536 °2--0.6441 °2
S-0.062 Å °-0.0469 Å °0.0568 Å °-0.1754 Å °0.071 Å °0.143 Å °-0.0103 Å °-0.141 Å °-0.0006 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 258
2X-RAY DIFFRACTION1allA259 - 260
3X-RAY DIFFRACTION1allS1 - 126

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