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- PDB-3tqr: Structure of the phosphoribosylglycinamide formyltransferase (pur... -

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Basic information

Entry
Database: PDB / ID: 3tqr
TitleStructure of the phosphoribosylglycinamide formyltransferase (purN) in complex with CHES from Coxiella burnetii
ComponentsPhosphoribosylglycinamide formyltransferase
KeywordsTRANSFERASE / Purines / pyrimidines / nucleosides / nucleotides
Function / homology
Function and homology information


phosphoribosylglycinamide formyltransferase 1 / phosphoribosylglycinamide formyltransferase activity / 'de novo' IMP biosynthetic process / cytosol / cytoplasm
Similarity search - Function
Phosphoribosylglycinamide formyltransferase / Formyl transferase, N-terminal domain / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoribosylglycinamide formyltransferase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 Å
AuthorsRudolph, M. / Cheung, J. / Franklin, M.C. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosylglycinamide formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2123
Polymers23,9691
Non-polymers2432
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Phosphoribosylglycinamide formyltransferase
hetero molecules

A: Phosphoribosylglycinamide formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4236
Polymers47,9382
Non-polymers4854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1980 Å2
ΔGint-24 kcal/mol
Surface area20360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.574, 117.498, 79.058
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-229-

HOH

21A-342-

HOH

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Components

#1: Protein Phosphoribosylglycinamide formyltransferase /


Mass: 23968.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Gene: purN, CBU_1737 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q83AY9, phosphoribosylglycinamide formyltransferase 1
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 3.27 Å3/Da / Density % sol: 62.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 1 M Trisodium citrate, 100 mM CHES, pH 9.5, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 13, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. all: 22613 / Num. obs: 22274 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.058 / Χ2: 1.053 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.97-23.40.4549451.103184.1
2-2.044.10.44810781.123197
2.04-2.084.70.3811031.065199.1
2.08-2.124.80.33911151.122199.3
2.12-2.174.80.27111140.988199.6
2.17-2.224.80.26510791.063199.3
2.22-2.274.90.2411141.073199.6
2.27-2.344.90.20711271.082199.7
2.34-2.44.90.18511081.116199.7
2.4-2.484.90.15311260.983199.9
2.48-2.574.90.13111110.9941100
2.57-2.674.90.11611250.9871100
2.67-2.84.90.09611231.0761100
2.8-2.9450.07711390.9981100
2.94-3.1350.06411181.0421100
3.13-3.3750.04611521.0181100
3.37-3.7150.03611281.11100
3.71-4.244.90.02911481.07199.9
4.24-5.3550.02811511.097199.5
5.35-504.70.02711701.009194.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→17.548 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8621 / SU ML: 0.23 / σ(F): 0 / Phase error: 20.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 1141 5.14 %Random
Rwork0.1847 ---
all0.1866 23347 --
obs0.1866 22206 98.58 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.955 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso max: 123.64 Å2 / Biso mean: 35.0807 Å2 / Biso min: 13.99 Å2
Baniso -1Baniso -2Baniso -3
1--4.1175 Å20 Å20 Å2
2--1.6095 Å20 Å2
3---2.508 Å2
Refinement stepCycle: LAST / Resolution: 1.97→17.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1645 0 14 182 1841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081698
X-RAY DIFFRACTIONf_angle_d1.0632309
X-RAY DIFFRACTIONf_chiral_restr0.073262
X-RAY DIFFRACTIONf_plane_restr0.005297
X-RAY DIFFRACTIONf_dihedral_angle_d12.373627
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 (%)
1.97-2.06210.25951310.21642446257793
2.0621-2.17060.28361530.19562626277999
2.1706-2.30630.22581360.19492605274199
2.3063-2.48390.26761350.209626562791100
2.4839-2.73310.21771680.201326122780100
2.7331-3.12660.21621300.183526702800100
3.1266-3.93190.21371430.169126932836100
3.9319-17.54840.21061450.17662757290299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.61470.68520.19411.5641-0.07040.80020.0973-0.13060.6986-0.0872-0.05610.0065-0.10570.0185-0.02530.2291-0.00080.04050.2003-0.09070.3313-0.303148.784938.2476
20.8456-0.25240.30061.05460.13840.1887-0.0262-0.1431-0.01040.1886-0.1208-0.04240.06760.07770.10440.20260.0083-0.01180.23430.01850.15696.498731.013535.2099
31.7697-0.7077-0.38460.6103-0.32830.7537-0.0623-0.27260.07670.1108-0.0311-0.0951-0.09730.2610.07470.18290.01280.00150.2221-0.00270.14733.949929.916329.2421
42.52450.4582-2.16021.4626-0.54191.85620.0468-0.51010.01040.1207-0.17490.1164-0.0350.4750.08270.1717-0.03020.03460.2565-0.00080.1588-9.855730.980641.2903
54.0083-0.2264-1.85310.0245-0.01952.185-0.3196-0.2061-1.3882-0.10180.1166-0.1480.48820.19430.35080.2919-0.00410.10850.2901-0.01820.4035-6.355122.590337.4633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 4:101)A4 - 101
2X-RAY DIFFRACTION2(CHAIN A AND RESID 102:140)A102 - 140
3X-RAY DIFFRACTION3(CHAIN A AND RESID 141:179)A141 - 179
4X-RAY DIFFRACTION4(CHAIN A AND RESID 180:204)A180 - 204
5X-RAY DIFFRACTION5(CHAIN A AND RESID 205:215)A205 - 215

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